Skip to main content

Full text of "Principles of Biology"

See other formats


1. Module 1: Science, Biology and Evolution 
1. Studio Biology - What is it? 
1. Studio Biology - What is it? 
2. Science as a way of knowing 
1. Science as a way of knowing 
3. Evolution 
1. Evolution 
4. Taxonomy and phylogeny 
2. Module 2: Ecology 
1. Introduction to Ecology and Ecosystems 
1. The Scope of Ecology 
. Ecology of Ecosystems 
. The Laws of Thermodynamics 
. Energy Flow 
. Biogeochemical Cycles 
. Biogeography 
Biomes 
8. Aquatic Biomes 
2. Population Ecology 
1. Population 
2. Population Growth 
3. Population Regulation 
4. Human Population Growth 
3. Community Ecology 
1. Community Ecology 
4. Ecological Research 
1. Ecosystem Experimentation and Modeling 
2. Nitrogen and Phosphorus Cycles 
3. Freshwater Biomes 
4. Population Growth Curves 


NOU RWN 


5. Introduction to Water Pollution 
3. Module 3: Cell Biology 
1. Introduction to Cell Biology 
1. Introduction to Cells 
. Prokaryotic Cells 
. Eukaryotic Cells 
. Protists 
. Fungi 
6. Eukaryotic Origins 
2. Tour of the Cell: Water, Carbohydrates and Lipids 


ui BR WN 


1. Atoms, Isotopes, Ions, and Molecules: The Building 


Blocks 
. Water: the Molecule of Life 
. Introduction to Biological Molecules 


. Carbohydrates 
. Lipids 


AuBRWN 


. Chemical Reactions of Biological Macromolecules 


7. Components and Structure of Plasmal Membranes 


3. Tour of the Cell: Proteins and Enzyme Function 
1. Proteins 
2. Enzymes 
3. Buffers and Enzymes 
4. Tour of the Cell: Nucleic Acids and Cell Cycle 
1. Nucleic Acids and Nucleotides 
. Cell Reproduction 
. DNA Replication 
. Prokaryotic Cell Division 
. Eukaryotic Cell Cycle 
6. Cancer and the Cell Cycle 
4. Module 4: Genetics 
1. Molecular Genetics: DNA to Protein to Phenotype 
1. ‘Transcription 


ui BW N 


2. Translation 
3. Connection Between DNA and Phenotype 
2. Meiosis and Mendelian Genetics 
1. Sexual Reproduction 
2. Meiosis 
3. Mendel’s Experiments 
4. Laws of Inheritance 
3. Variations on Mendelian Genetics 
1. Extensions of the Laws of Inheritance 
4. Population Genetics 
1. Population Evolution 
2. Population Genetics 
3. Formation of New Species 
5. Module 5: Energetics 
1. Cellular Energetics 
1. Energy and Metabolism 
. Thermodynamics 
. Potential, Kinetic, and Free Energy 
. Energy in Living Systems 
. Cell Membranes and Passive Transport 
6. Energy Requiring ‘Transport 
2. Photosynthesis 
1. Overview of Photosynthesis 
2. The Light-Dependent Reactions 
3. Calvin Cycle 
3. Cellular Respiration 
1. Overview of Cellular Respiration 
2. Glycolysis 
3. Oxidation of Pyruvate and the Krebs Cycle 
4. Oxidative Phosphorylation 
5. Metabolism Without Oxygen 
4. Bacteria and Fungi: Using Alternative Energy Sources 


ui BW N 


—_ 
-. 
a] 
=) 
= 
ig?) 
QD 
ld 
fmie 
oO 
=) 
1p) 
oO 
— 
Cd) 
= 
oO 
ie) 
a 

< 
Cu 
= 
jab) 
os 

1D 
a=) 
om 
oO 
aaa 
a>) 
— 

=) 
jab) 
=) 
an 
ay 
fmie 

=) 
fae 
(ae 


Metabolic Pathways 
2. Prokaryote Structure 
3. Prokaryotic diversity 
4. Kingdom Fungi 
6. Module 6: Plant Biology 
1. Evolution and Diversity of Plants 
1. Lichens, Protists and Green Algae 
. Early Plant Life 
. Bryophytes 
. Seedless Vascular Plants 
. Evolution of Seed Plants 
. Gymnosperms 
. Angiosperms 
8. Asexual Reproduction 
2. Plant Reproduction; Structure and Function of Plant 
Tissues 
1. The Plant Body 
2. Plant Sensory Systems and Responses 
3. Reproductive Development and Structure 
4. Pollination and Fertilization 
3. Interactions of Plants With Their Environment 
1. Root and Leaf Structure 
2. ‘Transport of Water and Solutes in Plants 
3. Nutritional Requirements of Plants 
4. Nutritional Adaptations of Plants 
4. Photosynthesis, Global Climate Change, and Food 
Production 
1. Photosynthetic Pathways 
2. Climate and the Effects of Global Climate Change 
3. Human Population Continues to Grow 
7. Module 7: Animal Biology 


NID OB WN 


1. Introduction to Animals 
1. Features of the Animal Kingdom 
2. Animal Tissue Types 
3. Sponges and Cnidarians 
4. Flatworms, Nematodes, and Arthropods 
5. Mollusks and Annelids 
6. Echinoderms and Chordates 
7. Vertebrates 
8. Homeostasis 
2. Material Acquisition and Transport 
1. Digestive Systems 
2. Digestive System Processes 
3. Nutrition 
4. The Circulatory System 
5. Systems of Gas Exchange 
3. Internal Communication and Coordination 
1. Nervous System 
2. Endocrine System 
3. Digestive System Regulation 
4. How Animals Reproduce 
4. External Communication and Coordination 
1. The Integumentary System 
. Sensory Systems 
. Reflexes and Homeostasis 
. Viruses 
. Innate Immunity 
6. Adaptive Immunity 
5. Adaptations to Land 
1. Urinary System 
2. Musculoskeletal System 


wu BW N 


Studio Biology - What is it? 
An introduction to the format of Biology 198 - Principles of Biology, taught 
at Kansas State University 


The Studio Format 


Introduction 

"The first principle is that you must not fool yourself - and you are the 
easiest person to fool." Richard Feynman, American physicist and Nobel 
Prize winner, delivering the Caltech commencement address, 1974 


Welcome to Principles of Biology, Kansas State University’s innovative 
introductory biology course. Because this course is almost certainly unlike 
any course you have taken before, we need to spend a little time to 
introduce it, and tell you why this course is a great way to learn about 
biology. 


Unlike the traditional lecture & lab introductory biology courses at most 
universities, Biology 198 at K-State is a studio-format course, combining 
lecture and lab into the same class period. There are some unique things 
about studio courses, and especially this one. Our studio model involves 2 
separate 2-hour sessions per week, with a maximum of 78 students in the 
studio; thus you will spend about 4 hours per week in the studio classroom. 
So it is important to understand that you are in a studio course, which is not 
a lecture, and not a lab, but is actually a hybrid of lecture and lab. Although 
it is an introductory course, it was developed with input from all the faculty 
members in the Division of Biology. There are usually two faculty 
members, two GTAs and one or more undergraduate practicum student 
instructors per 80 students in each section. 


Why do we teach this course this way? Because we believe in education, 
and also in giving KSU students a lot of education for their tuition dollars. 
The studio format has been shown to be a very effective way for us to help 
you learn about biology. In fact, it is about twice as effective as the 
traditional lecture/lab course in terms of your learning and retention of the 
material. So that’s why we teach it this way. 


It is also unique in that the faculty members teaching this course can 
include anyone in the department, including full professors. Introductory 
science courses, in particular, tend to be taught by graduate teaching 
assistants here, and at other institutions. If they are taught by a full 
professor in Biology 198, many freshman students will not have another 
course taught by a full professor until their junior or senior year. At many of 
our peer institutions, introductory biology courses are taught with a single 
instructor lecturing to 500-800 students, accompanied by a lab taught solely 
with graduate students. That’s a relatively inexpensive way to teach 
introductory science courses, but also a relatively ineffective way. If you 
take advantage of the significant resources (both personnel and material) 
that the Division of Biology devotes to this course, you will learn a lot of 
biology. Equally importantly, you will learn how to study and be successful 
in a university environment. That’s another advantage of the studio format! 


Course materials 


Two items are essential to your successful learning in this course, both of 
which are designed to maximize learning in the studio environment. The 
first is the free electronic textbook, which you are reading now. The second 
is the Principles of Biology Studio Manual, which must be purchased from 
the KSU Biology Graduate Student Association. It may look like a lab 
notebook, but is actually something quite different. The studio manual is 
analogous to your lecture notes in a standard lecture class; it is simply 
YOUR record of what you do in the studio. What you see, do and hear 
during your time in class will be recorded in your Principles of Biology 
Studio Manual. More importantly, it is not analogous to a lab notebook ina 
lab class. You do not need to turn it in to be graded (just like nobody grades 
your lecture notes in a lecture class!). So please treat that studio manual, 
which is a required text for this course, like you would your lecture notes in 
any other class. Read it over before the next class, mark down any questions 
you might have, and make sure you get a copy of the notes from another 
student if you have to miss a studio class. 


Course and testing structure 


The course is divided into 7 units, each with four or five class periods that 
are devoted to those units. There are tests on all 7 units, and the dates for 
those tests can be found on your course syllabus (link). You will start with 
an Introduction to Science and Biology (including two classes on 
Evolution), then go immediately into the study of Ecology and Ecosystems. 
After gaining this large-scale perspective, you will move to the study of 
living things at the smallest scale (molecules and cells), and then move up 
to the organism level (Genetics, Energetics). The final two units are more 
traditional (Plant Biology, Animal Biology). The final exam, at the end of 
the semester, is not a comprehensive exam; it covers only the last unit 
(Animal Biology). But all of the learning that you have done in prior units 
will be very important in your understanding of the concepts covered in that 
final exam 


The test questions are all written to evaluate your knowledge of the unit 
Objectives. More importantly, the objectives for each class period are 
provided to you at the very beginning of each section of the studio manual. 
So if you want to know “What do I have to know for the tests?”, the simple 
answer would be “the Objectives for that unit”. You will gain an 
understanding of these objectives in many ways, not only from this 
electronic textbook, but from the studio exercises, the web pages for this 
class, and from discussions with your fellow students both inside and 
outside the classroom. In addition we have prepared Study Guides that are 
also based on the Objectives. For each of the day’s Objectives, we provide a 
detailed listing of all the places (e.g. textbook, studio exercise, web page, or 
some combination of those) where you can get the information needed to 
master that Objective. If you spend your time in the studio wisely, and study 
with those Study Guides regularly (not just the day before the exam!), you 
should have a very clear understanding of the material that we think you 
should be learning in this class. Each question on each exam is written with 
one of those Objectives in mind, so it should be obvious that the Objectives 
are the key item on which to focus your efforts. 


Your responsibilities 


There will be readings in the textbook for every class day (except for the 
very first day of class); those reading assignments are listed in the Studio 


Manual, right after the Objectives for every class period. The textbook 
readings are an introduction to the topics for the studio exercises that day, 
so you need to read them BEFORE coming to class each day. In order to 
assure that you do the reading, there will be a short quiz over the reading 
material for every class period. By the end of the semester, the points for 
these quizzes add up to approximately the same value as a unit exam. The 
points should provide some incentive, but as you learn more about this 
course you should also figure out that learning in the studio classroom is 
more efficient if you have a good understanding of the material covered in 
the reading for that day. And more efficient learning in the classroom 
translates to better scores on the unit exams! 


In addition, your instructors will track your attendance in the studio; 
attendance is strongly recommended for this class. Interacting with your 
instructors and fellow students is an important component of the class, and 
we have excellent data which prove that missing multiple classes is highly 
correlated with lower exam scores, and lesser learning and retention. We 
really want you to learn biology, but you can’t do that if you are not in 
class. So to make sure that you take full advantage of the learning 
opportunities in the studio, we give an attendance bonus at the end of the 
semester. Please see the syllabus for more details. 


Your success in this course, both in terms of amount learned and in terms of 
a good grade, is assured if you understand the format of the course, do the 
assigned readings and attend the studio sessions faithfully, and spend at 
least as much time studying outside the classroom as you spend inside the 
classroom. You are responsible for learning, just as you are responsible in 
every class you take. But the difference in this class is that we do 
everything we can to provide the resources and the environment where 
learning is maximized. 


Instructor responsibilities 


Your studio instructors will deliver a brief (10-15 minute) introductory 
lecture at the start of each class day, and an equally brief wrap-up session at 
the end. In between those two lectures, you will be working with your 
fellow students on the studio exercises for that day. During that time the 


instructors will circulate in the studio, asking questions, answering 
questions, and generally helping you learn the material. Please take 
advantage of this incredible opportunity to interact, one on one, with your 
faculty and GTA instructors. If you have a question, don’t be shy. If you 
want to know if your class notes (i.e., the stuff you are writing in the Studio 
Manual) are accurate, ask an instructor. Their job is to help you learn the 
material, and they can help a lot more if they know what your questions and 
concerns might be. 


Your studio instructors will also be responsible for grading the daily quizzes 
and recording those grades, usually in a course that they set up on K-State 
Online. If you are not familiar with K-State Online, don’t worry. It is our 
course Management system, and it is very easy to navigate. Your studio 
instructors will not be responsible for writing the biweekly unit exams. 
Since there are 10 sections of this course each semester, it is better (and 
more fair) if all students in all sections take the same exams. So those 
exams are written by the course coordinator, and all exam questions are 
vetted by faculty members who are teaching in one or more sections in a 
semester. The first 6 unit exams are administered on Monday evenings (see 
syllabus for the exact dates), and the final unit exam is administered on 
Thursday morning during finals week. Grades for these exams will be 
recorded on K-State Online as well, so that you have ready access to your 
grade information. 


Helpful hints 


¢ Read the assigned material before coming to class. 

e Don’t skip class. 

e Take advantage of the learning opportunities afforded in the studio 
(your fellow students, the instructors, the practicum students, the 
studio exercises, etc.) every time you are in class. 

e Take good notes and read over your notes in the studio manual within 
24 hours after every class. 

e Use the study guides and concentrate on the Objectives when you 
study for the unit exams. 

e Study a little bit every day rather than cramming the day before the 
exams. 


e Ask lots of questions, and be prepared to answer lots of questions. 
¢ Don’t fall behind, but if you do, make every effort to catch up as soon 
as possible. 


Science as a way of knowing 
The scientific method as it applies to biology 


Science as a way of knowing 


"We absolutely must leave room for doubt or there is no progress and no 
learning. There is no learning without having to pose a question. And a 
question requires doubt. People search for certainty. But there is no 
certainty." — physicist Richard Feynman, in a lecture at the Galileo 
Symposium, 1964. 


Introduction 


What is “Science”? Everyone probably has some idea of what the word 
means, but have you ever really thought about it? If so, here are some 
questions to consider. 


e Is science a body of knowledge? 

e Is it the same thing as “truth”? 

e Is it a way to understand everything, or just a few things? 

e Is it a process, and if so, can everyone do it? Or do you have to be 
highly intelligent, highly trained, or both, if you want to understand 
science? 


Hopefully by the end of this course, or even by the end of this first module, 
you will have some good answers to those questions, and will be well on 
your way to thinking like a scientist (at least for this class!). Let’s start with 
the title of this chapter — Science as a Way of Knowing. That description is 
from the title of a great little book by biologist John A. Moore, and is 
actually a pretty good answer to the question of “What is Science?” Science 
is both a body of knowledge, and an evidence-based process for generating 
that knowledge. The word itself comes from a Latin term, scientia, which 
means knowledge. But science is also about a particular kind of knowledge 
- knowledge about the natural world. In addition, the process of “doing 
science” can only help us gain additional understanding about the natural 
world. It is of no use to us if we want to understand the supernatural. For 
that we need other ways of knowing. 


There are also some other aspects of science which you need to know, as 
you move toward a better understanding of both the scientific knowledge 
base and the scientific process. 


Science 


e requires interaction with the natural world in terms of observation, 
detection, or measurement. 

e is objective, or evidence-based; that evidence, or a repeated 
demonstration of the evidence, must be available to everyone. 
Scientists generally don’t just “take your word for it.” 

e requires independent evaluation and replication by others. 

e leads to conclusions that are always provisional, i.e., they will be 
rejected or modified if new observations or measurements show that 
they are false. 


There are, of course, other "ways of knowing". How do we know what we 
know? People who study knowledge (yes, there are such people, and they 
are in the branch of philosophy known as epistemology) often classify that 
knowledge based on the source of the knowledge. In mathematics and logic, 
for example, we can point to things that we know are "rationally true". In 
science, we focus on things that are "empirically true", i.e., based on 
evidence that we can see, hear, touch, etc. In religion, and, to a lesser extent, 
in history, we focus on "revelational truth", or knowledge that comes from 
another source that we accept as true, based on our assessment of the 
reliability of the source. So the subjects that you might study at this 
university can depend on different sources for the knowledge that you will 
be gaining. In this class we will focus, as noted above, on objective 
evidence obtained from observations of the natural world, and we will use 
some very specific terms to describe how those empirical observations form 
the basis for scientific knowledge and understanding. 


The process of science 


So how does this process work? The processes that generate scientific 
knowledge are known as the scientific method. But even as you learn this 
method, it is important to realize that this is not a set recipe or process that 


MUST be followed in all cases. The scientific method is best understood as 
a statement of the core logical principles underlying how science works. 
The process of science always uses these core logical principles, but any 
individual scientific enterprise might not adhere exactly to the method 
outlined below ([link]). 


The Basic Scientific Method 


Formulate 
Hypotheses 


I 


Observation & 
Experimentation 


Accumulated Data 
or observations 
i" = 


— 
=> Theory 


The Scientific Method — 1) Observations are used to formulate the 
2) hypothesis, which is then 3) tested with experiments or new 
observations. The 4) new data contribute to the pool of 
observations, and also are used to refine the hypothesis as needed. 
Eventually the accumulated data allow one to make a 5) 
conclusion, which can contribute support for an existing 6) theory, 
or in some cases, support for a new theory. In all cases theories 
can be used to generate new testable hypotheses, which is why we 
say theories are both explanatory and predictive. 


All science starts with an observation, or set of observations, about the 
natural world. You might observe a pair of male elk fighting in a high- 
country meadow in Colorado, for example. The next step, if you want to 
think about this scientifically, is to formulate some hypothesis to explain 
that observation. A hypothesis is a statement that is simply an educated 
guess about the cause(s) of the observed phenomenon. In order for that 
hypothesis to be useful in a scientific sense, however, it must have some 
additional characters. A scientific hypothesis must be testable, and it must 
be falsifiable. It does no good to generate a hypothesis that you cannot test 
in the real world. Thus it would not be a scientific hypothesis if you stated 
that the elk were fighting because invisible men in an invisible spaceship 
parked on the far side of the moon were controlling these elk with 
undetectable brain waves. That might be the actual explanation, but you 
can’t test it, and you can’t falsify it. 


A good scientific hypothesis lends itself to making testable predictions; if 
the hypothesis is true, then X must be true. In this case you might state 
generate this hypothesis — these are male elk, and they are fighting for 
control of a herd of female elk. Immediately some predictions come to 
mind. If this hypothesis is true, you should be able to detect that these are 
male elk. Without getting too close, you can see that they have antlers, and 
previous work by other scientists (part of the set of accumulated 
observations that you are relying on) has shown that only male elk have 
antlers. Prediction confirmed. Another prediction might be that there should 
be one or more female elk nearby, and that these females would eventually 
go with the male who wins the fight or drives off the other male. You look 
around, and you see a herd of 10 or so female (antlerless) elk watching the 
spectacle. Another prediction confirmed. You will have to wait until the 
fight is over before you know if the prediction about the females staying 
with the winner is confirmed. But you have two predictions confirmed, and 
so far your hypothesis is supported by the evidence. More importantly, it 
has not been falsified. All of the data so far support it. 


This brings up another important aspect of the process of science. In this 
case you made predictions and confirmed them with additional 


observations. You didn’t do anything to the subjects; you merely observed 
them more closely. That is a valid approach. An equally valid approach 
would be to test your hypothesis by means of experiments. Experiments 
are manipulations of the experimental system, followed by additional 
observations. In this case, for example, you might hypothesize that the male 
hormone testosterone is causing the elk to fight. One prediction from that 
hypothesis would be that injection of testosterone into female elk (which 
don’t normally produce testosterone) would lead to aggressive behaviors in 
the female elk. You would also predict that male elk, deprived of 
testosterone, would be less aggressive. You might be able to come up with 
some other predictions from this hypothesis that could be tested with other 
experiments. You would have to capture some elk (male and female) to do 
the experiments needed to test these predictions, of course. That could be 
tricky, or dangerous, and you might need to hire and train help. Or you 
could look for similar behaviors in smaller, more easily handled animals 
such as mice or rats, and do the same experiments with those creatures. 
Both of these approaches, using observations or using experiments, are 
scientifically valid, as long as your hypothesis is testable and falsifiable. 
Furthermore, as you will learn many times in this course, there are other 
aspects of the experimental approach, involving concepts like sample size, 
variables, and controls, which you will need to consider as well. We’ |l 
save the discussion of those until a bit later, after we conclude our 
consideration of the general scientific method. 


If you look at ({link]), you will see that multiple tests of the predictions lead 
to an increase in the number of observations. Any test of the hypothesis, no 
matter if it confirms or disconfirms the hypothesis, adds to our knowledge 
base. Generating new knowledge is one of the exciting parts of doing 
science, in fact. All of these observations can be used by future generations 
of scientists to test future hypotheses. 


You’ll also find another important word in ({link]), and that is the word 
theory. In regular conversations, people outside of science often use this 
word to mean an unproven or unsupported explanation, a wild guess. As 
you learned above, in science that description would be more appropriate 
for the word hypothesis. In science, a theory means something quite 
different. A theory is a statement or set of statements that explains some 


aspect of the natural world that is supported by substantial amounts of data 
from diverse lines of investigation. The statements that form a theory are 
NOT "wild Guesses" but are often hypotheses that have been tested many 
times. Therefore, a theory has predictive power and those predictions can be 
tested. If a prediction is falsified, it does not mean the theory is false, it 
means the hypothesis needs to be reworked. There are many theories in 
science; examples relevant to the study of biology include the germ theory, 
the cell theory, plate-tectonic theory, and of course the grand unifying 
theory of evolution. All of them are well supported by incredible numbers 
of observations; all of them are considered the best available explanation 
for a diverse set of observations. 


In addition, as shown in ({link]), you can see that just as observations lead 
to predictive hypotheses, theories can lead to predictive hypotheses as 
well. In fact, one of the hallmarks of a theory is that it provides a solid 
framework for generating hypotheses and making predictions. Scientists are 
confident in the explanatory power of theories, and thus are comfortable in 
using them to construct hypotheses, design experiments, and frame the 
interpretation of the data generated by those experiments. Just as a scientific 
hypothesis is useless if it cannot generate predictive hypotheses, a theory 
must serve as a framework for hypothesis building and testing. And just as 
the predictions of the hypothesis must be borne out by new observations if 
the hypothesis is going to be accepted, predictions from a theory must be 
supported by the observations if the theory is to continue to serve as the 
best available explanation for a vast set of observations. 


Not shown in that figure, but implied nonetheless, is the fact that the 
observations must be repeatable. Other scientists, working in other 
locations, need to be able to do similar experiments and get the same 
results. That is what is meant by the statement that science is objective, not 
subjective. Another scientist has to be able to get the same results as you, 
and vice versa. Again, the history of science has thousands of examples 
where a new and exciting result was announced, but eventually forgotten 
when other scientists could not get the same result. Recent ones include the 
phenomenon known as “cold fusion”, or the identification of a virus that 
was thought to cause Chronic Fatigue Syndrome (CFS). In all of these cases 
the original observation was found to be flawed in some way, and 


subsequent work, either by the original observers or by others, revealed the 
flaws and debunked the explanation. 


Finally, it is important to remember that all scientific conclusions are 
provisional. In other words, a scientific conclusion is accepted as the 
current best explanation, but with the understanding that future 
investigators could make observations that might negate or modify the 
conclusion. So it is likely that some of the things that you will learn in this 
class are wrong, or at least incomplete. We still expect you to learn them, 
since they are the current best explanation, but it is almost certain that 
something in this textbook, or in the other materials for this course, will be 
shown by future scientists to be erroneous or incomplete. Who knows, you 
might be the scientist who does the work that reveals the error. Scientists 
actually dream about being the person who overturns a long-established 
notion, since that often means that their work will be remembered, and may 
even appear in future biology textbooks. One example of overturning a 
long-established concept, and ensuring a place in future textbooks, can be 
found in Louis Pasteur’s experiments, described below 


Experiments and controls 


As mentioned above, a common approach to generate new scientific 
knowledge is to perform experiments, where the scientist changes the 
situation and then observes the effects of these changes. In keeping with the 
scientific method, this starts with an observation, from which the scientist 
generates a hypothesis. The hypothesis leads to a testable prediction, 
followed by experiments based on that testable prediction. Let’s look at one 
of the most famous experiments in all of biology as an example. 


¢ 


| Broth without contamination without contamination 


‘ 


‘Grgenismagrew | grew 


Pasteur's test of the hypothesis of spontaneous generation [By 
Carmel830 (Own work) [Public domain], via Wikimedia 
Commons]. Pasteur attempted to explain the observation that 
organisms (molds and bacteria) appeared in meat broth that had 
been boiled. His hypothesis was that these organisms came from 
the air, rather than from spontaneous generation. That hypothesis 
would predict that organisms would not appear if the meat broth 
was not exposed to air. He boiled the broth in flasks with long 
necks; air could not enter past the fluid that was left in a U-shaped 
section of the neck of the flask. As a control he boiled broth in 
other long-necked flasks, but then broke the necks off so that room 
air (and any microbes in that air) could fall on the broth. No 
organisms grew in the flasks with intact necks; organisms were 
found in abundance in the flasks with the broken necks. 


It was widely believed in ancient times that living things arose 
spontaneously if conditions were right. One of the observations that led to 
this belief was that molds, bacteria, maggots and other life forms appeared 
if one left a piece of meat out in the air for a while. This concept of 
spontaneous generation was tested in 1860 by Louis Pasteur, using an 
experimental setup diagrammed above ((link]). Pasteur heated meat broth, 
in glass flasks, to a temperature where he imagined that no living things 
were left alive in the broth. If he left this broth out in the open, it developed 
active bacterial and mold growth, an observation which was consistent with 
the notion of spontaneous generation. But Pasteur, having recently learned 
about microbes, suspected that the mold and bacteria arose not from 
spontaneous generation, but from microbes present in the air. So he devised 
a set of experiments to test this hypothesis: Living microbial cells present 
on dust particles in the air are the source of the living cells growing in the 
heated meat broth. 


What prediction could one make with this hypothesis? You can probably 
think of a couple, but the one that Pasteur came up with was that if the meat 
broth was in a vessel which excluded cells dropping into it from the air 
above, there would be no bacterial or mold growth in the broth. So he 
heated batches of broth in long-necked glass flasks until he thought the 
broth was sterilized, and also heated the necks of the flask to allow him to 
bend them into an “S” shape. The ends of the flasks remained open to the 
outside air, but dust settled in the trap in the neck of the flask and did not 
reach the surface of the meat broth. In other experiments, he broke off the 
neck after heating the flasks, allowing dust particles to settle on the broth, 
or waited a few days and then tilted the flasks so that the broth came into 
contact with the dust trapped in the bottom of the trap in the neck of the 
flask. Then he observed the results. Just as importantly, he repeated the 
experiments several times to make sure that his observations were correct. 


We’ve already discussed the hypothesis, and one prediction, above. But 
what are some other important aspects of this experimental approach? One 
is the concept of a variable. A variable is some condition of the 
experimental setup that can be manipulated by the experimenter. Ideally, the 
experimenter should change only one variable at a time (keeping all other 
conditions identical); this makes interpretation of the results a lot more 


straightforward. What was the variable in Pasteur’s experimental setup? In 
this case, the variable was access of dust to the surface of the broth. In 
flasks that were left open, access was allowed. In the flasks that had an 
intact S-shaped trap in the neck, access was not allowed. Pasteur also 
manipulated this variable by tilting the S-shaped flasks so that accumulated 
dust could contact the broth. 


The other important part of this experimental approach is the concept of 
control experiments, also known by a shorter term as just controls. A 
control experiment is a setup where the variable is not introduced, so that it 
can be directly compared to the experimental situation where the variable 
(access of dust particles to the broth) is included. So a control experiment 
for Pasteur's incubation of broth in an open-necked flask would be 
incubation of broth in the S-necked flasks. If the variable is introduced by 
tilting the flasks, the control would again be the S-necked flasks. All other 
conditions (heating temperature, amount of broth, size of flasks, etc.) were 
the same in the experimental and control situations. The only thing that was 
different was a single variable (access of dust particles to the meat broth), 
because that was the hypothesized source of the living cells that grow in 
meat broth left out in the open. A single control experiment is usually all 
that is needed if there is only a single experimental variable being 
manipulated. 


But it is not always possible to simplify a system so that there is only one 
variable. In those cases, as you will learn in the studio exercises for this 
class, you might need multiple control experiments. Experiments and 
controls will also be repeated before the investigator reports the results. It 
will be described in a way such that other investigators can readily repeat it 
as well. In some situations the results will be subjected to statistical 
analysis, although this was not necessary in Pasteur’s experiment. Statistical 
analysis is critical in many scientific approaches, particularly in studies 
involving hypotheses about human subjects (e.g., the hypothesis that 
smoking causes lung cancer), where experimental manipulation of the 
subjects is difficult or impossible. A scientific experiment, no matter how 
the results are analyzed, should lead to a conclusion that either supports, or 
fails to support, the hypothesis. Finally, the experimental results should lead 
to additional hypotheses, and additional predictions, that can generate 


further support (or lack of support) for the hypothesis. Try to think of a few 
additional experiments that you might have suggested to Louis Pasteur if 
you were alive in 1860, and if you could speak French! 


Other aspects of science 


The characteristics inherent in the scientific process lead to another 
property of science, and that is that science is self-correcting. By that we 
mean that errors can be made, but that continued application of the tools 
and processes of science will usually lead to elimination of the errors and a 
more accurate understanding of the natural world. Science never really and 
finally proves anything to be true; it can, however, prove things to be 
untrue. To some people, in fact, that characteristic of science, its fluid and 
changing nature, is maddening. If you require solid ground to stand on, and 
immutable truth in all aspects of your life, you probably shouldn’t become a 
scientist. If you find excitement in being part of an enterprise that is 
constantly changing the extent, and even the nature, of knowledge, then you 
have some of what it takes to be a scientist. But even if you don’t become a 
scientist, a bit on scientific knowledge, and a bit of practice with the 
scientific process, will help you understand the things you need to 
understand in order to make intelligent decisions about many things, such 
as health care, climate change, or other concepts that are in your future. 


Science is also a curious mix of intuitive and counter-intuitive behaviors. 
You practice the scientific method intuitively every day, whether you realize 
it or not. If you flip on the light switch in your bathroom in the morning, 
and the light doesn’t come on, you probably take a scientific approach to 
solving that problem. You might hypothesize that the bulb is burnt out, and 
if that hypothesis is correct, replacing the bulb should solve the problem. So 
you do that experiment, and replace the bulb, and the light goes on, and you 
can continue with your daily activities blissfully unaware of the fact that 
you acted scientifically already that day. Intuitive science in action! 


But some aspects of science, and particularly the scientific process, are not 
intuitive. All of us have the ability to think that our explanation of some 
phenomenon is correct, even if there are other observations that contradict 
that explanation. In fact, we often search for additional evidence to confirm 


our conclusion, and ignore any evidence that we might find that casts doubt 
on the conclusion. This is known as confirmation bias, and is particularly 
strong in situations where we have an large emotional or financial stake in 
the conclusion. For example, you might consider yourself a pretty good 
basketball player. So when you have missed 10 shots in a row, you keep 
shooting until you make a shot, and then you feel better about your belief 
that you are a good basketball player, even if those shooting percentages 
contradict that belief. Or you might make a visit to the chiropractor when 
your neck hurts, and the chiropractor might make your neck feel better. But 
a few days later, when it hurts again, you might not take this as a sign that 
chiropractic manipulation is not a cure. You might go back to that 
chiropractor, to have the same manipulation, because you have already 
invested money there, and you’d like to think that you are not wasting your 
money. Confirmation bias, of the active sort rather than the passive version 
in the previous examples, is particularly evident in people who buy into 
conspiracy theories. They seek out others with the same beliefs, or they 
only look at websites that are dedicated to that belief. It’s only human 
nature that people like to hear what they think they already know. As a 
character in Terry Pratchett’s Discworld series observes, “...what people 
think they want is news, but what they really crave is olds...Not news but 
olds, telling people that what they think they already know is true.” We all 
like to think that we know everything that we need to know, and scientists 
are no exception. 


So scientists have to actively guard against confirmation bias. If a scientist 
has an hypothesis, she has to come up with predictions and experiments that 
will disprove that hypothesis. If the experiments indicate that the hypothesis 
is wrong, the scientist has to abandon that hypothesis and generate a new 
one, and it has to include the results of those disconfirming experiments. 
This is a very difficult assignment, and certainly goes against lots of human 
impulses. As the physicist Richard Feynman wrote, “The first principle is 
that you must not foolyourself, and you are the easiest person to fool.” 
Every good scientist has abandoned many more hypotheses than he or she 
has confirmed; science teaches humility that way, for certain. Scientists 
must be able to change their minds if observations warrant it; there is no 
shame for a scientist who admits being wrong. Exactly the opposite, in fact. 
There are many sad examples of individuals who hung on to a hypothesis 


too long, and ended up with a tarnished reputation. But as we all know, 
admitting you are wrong is difficult for most people, and scientists are 
human too. 


The science of biology 


It’s now time to shift from a discussion of science in general to the specific 
scientific discipline that you will be learning about, biology. Biology is the 
study of life. that naturally leads to the question — What is life? Suprisingly, 
that has proven to be a difficult question to answer in just a few words! 
Most textbook-level definitions of life are merely a list of characteristics; 
anything that exhibits all of those characteristics is said to be alive. Here’s a 
typical list. 


Living things: 


e Respond to the environment. 

e Assimilate and use energy from their environment. 

e Maintain a relatively constant internal environment, even as the 
external environment changes (homeostasis). 

e Reproduce (at the level of organisms) and can evolve (at the level of 
populations). 

e Are highly organized, relative to their environment. 


These are general characteristics, and might describe all organisms, even 
those which have not yet been discovered yet (e.g., those on other planets or 
solar systems). Until those organisms are discovered and studied, however, 
that statement is provisional. In addition, scientists have discovered that all 
living things discovered to date (i.e., the ones on this planet).are composed 
of one or more cells, and have DNA as their hereditary/genetic material. 
Some textbooks include these characteristics in their definition of life as 
well. More importantly, the commonality of DNA as the genetic molecule 
in all known life forms is strong evidence that all living things on this 
planet are related, i.e., they have a common ancestor. A putative common 
ancestor was a prediction made by Charles Darwin when he elucidated his 
theories about evolution and natural selection. The fact that his prediction 


proved to be correct is one (of many) pieces of evidence that support that 
theory. You’ll learn about some of the other evidence later in this course. 


One productive way to study and understand living things is to recognize 
that there is a biological hierarchy, which is basically an organizational 
concept map that allows us to focus on various levels of life. 


Biosphere Life on Earth 


= 


All the organisms plus 


Ecosystem = bees ‘ 
ate i | physical components 


cy 


All the organisms of 
a prairie: animal, 
plant, fungus, etc. 


Community 


= 


Population Bison population 


= 


Organism A bull bison 
Organ System ‘ J Circulatory system 
Heart 


>is 


Tissue Cardiac Muscle tissue 


cs 


Cell Cardiac Muscle cell 


= 


Macromolecule an Myosin V 
Tt, 


u oO 
\n—t 
Molecule H~ Non Amino acid (Valine) 
tt H3C~ ~ CH; 
oe? 
{ / \ 4 . 
Atom [( @ )F Nitrogen Atom 


The organization of life. Work by Eva Horne. 


This hierarchy ([link])extends from atoms and molecules, through cells, 
tissues, organs, organ systems, organisms, populations, communities, and 
ecosystems all the way to the biosphere (Planet Earth and the living 
organisms populating it). Biologists often focus on one or another of these 
levels, simply because it is far easier to study one level than to try to 
understand the entire spectrum, and the interactions between those levels. 
But all biologists recognize that there ARE many interactions between these 
levels, and those interactions lead to some very interesting and important 
processes as well. 


Consideration of this hierarchy, coupled with the difficulty in coming up 
with a simple definition of life, leads some scientists to another perspective 
as well. These scientists argue that it is pointless to try to define life. If life 
arose from self-replicating chemical systems, which is the working 
hypothesis in the field of science known as abiogenesis, and if there is a 
continuum running from atoms to molecules to cells, etc., then it is not 
possible to point to some arbitrary place on the continuum and define it as 
“living”. Nobel Prize-winning abiogenesis researcher Jack Szostak writes” 
None of this matters, however, in terms of the fundamental scientific 
questions concerning the transitions leading from chemistry to biology.” 
Indeed, as you come to learn more about viruses in this course or elsewhere, 
you will probably have some sympathy for this perspective. Are viruses 
alive? Or would it be better to say that they are somewhere along this 
continuum, and bypass that question altogether? 


As you proceed to learn biology in the studio classroom this semester, you 
will expand your understanding of the details underlying those 
characteristics of living things. For example, in regard to organisms 
responding to the environment, you will learn some of the ways that 
bacteria, plants and animals sense and respond to environmental conditions. 
You will learn how bacteria, plants and animals reproduce, and how that 
process of reproduction is integral to the process of evolution. You will 
learn about cells and tissues and organs, all of which are highly structured 
and organized arrangements, and how energy is obtained and expended so 
that these organized structures can be produced and maintained. Hopefully 
you will come to the realization that life, in all of its diverse incarnations, is 
amazing. Which is why biologists continue to study it! 


Evolution 
An introduction to evolutionary theory, summarizing some of the key lines 
of evidence in support of the theory. 


Evolution 


"How stupid of me not to have thought of that." — Thomas Huxley, after 
reading Darwin’s Origin (On the Origin of Species by Means of Natural 
Selection, or the Preservation of Favoured Races in the Struggle for Life). 


Introduction 


What is Evolution? Surely everyone has heard the word, and perhaps a lot 
of other words to describe it, but do you really know what that word means, 
in the context of biology? Here are a few common notions about evolution. 
How many do you agree with? 


1. Evolution has never been observed directly. 

2. Evolution is only a theory, and has not been shown to be a fact. 

3. Evolution means that life originated, and living things change, 
randomly. 

4. Evolution is progress; organisms get “better” and more complicated 

whenever evolution occurs. 

. Evolution means that individual organisms change. 

6. In order for evolution to occur, the offspring of some organisms will 
have to be radically different from the parental organisms. 


Ol 


If you said that all of these statements are false, then you have a good 
understanding of evolution. They are indeed all untrue. However, this is a 
list of some fairly common misconceptions about evolution, and many 
people in the world (and particularly in the USA) share one or more of 
these misconceptions. It is likely that you think that some or all of these 
statements are true. One of the hardest parts of learning is to undo a well- 
established misconception, so if you do think that one (or more) of those 
statements is true, this chapter might be a bit harder for you. But it will be 
worth the effort, since, as you will learn below, evolution is the guiding 
framework for modern biological science. Once you have a good 


understanding of evolution, and the mechanisms that drive it, you will be 
well-poised to learn and understand the biology that comes in the rest of 
this course. 


Evolution — what is it? 


The biological world is extremely diverse. In fact, that is one of the most 
powerful realizations that come from the study of biology, or even just from 
being an observant person in the world. Living things range from the 
microscopic bacteria to the immense blue whale. They have a diversity of 
life styles and metabolic capacities, from photosynthetic creatures who can 
make their own food from carbon dioxide gas, to predatory creatures, all the 
way to parasitic creatures who have some of the most complicated life 
styles of all. Within any one of these groups, there is also astounding 
diversity. Open any field guide, whether for birds, mammals, flowering 
plants, or mushrooms, and you will be confronted with an abundance of 
colors, sizes, shapes and behaviors. Even within a single species, say Homo 
sapiens, there is diversity. Look around your classroom and you will see 
people with a wide variety of skin colors, hair colors, eye colors, heights 
and weights. This diversity is a fact, and for many millennia, human beings 
have been trying to come up with explanations for that well-observed fact. 


You are probably familiar with some of these explanations. Many ancient 
peoples imagined that the world was created in the form that exists now, 
and that blue whales, pythons, and lilac bushes were created and unchanged 
since that creation. This is known as typology; every species conforms to an 
ideal and unchanging type, and all members of the species are true to that 
type. Wolves are a type, and all wolves (within certain parameters) were 
considered to be similar to all other wolves, but not similar to foxes, and 
even less similar to lions. And all of these creatures had ancestors who were 
also true to the type. Once it became clear that there had been creatures, 
preserved in the fossil record, unlike any creatures seen today, other 
explanations were needed to account for these new observations. When it 
became clear, from geology, that the earth was very ancient, and had been 
in existence for millions and even billions of years, other explanations 
became even more satisfactory. When it became clear, from studies of 
comparative anatomy, that many creatures shared anatomical and 


developmental similarities, even though they were of different types, other 
explanations became obvious. 


We won’t go through the many explanations for the diversity of life that 
have been proposed and been discarded over the centuries. There are lots of 
places where you can read about that historical progression, and it is 
interesting, for sure. Rather we will get to the explanation that is the most 
widely accepted scientific explanation today, and show how this 
explanation is supported by evidence, and also leads to predictive 
hypotheses that can serve as a further test of the explanation. That 
explanation is known as the Theory of Evolution. 


So we have a lot of observations to explain, and in this case those 
observations are that there are a lot of diverse organisms on the planet, and 
that they change over time. Those are observed facts, and can be 
categorized under the broad umbrella of "evolution". As discussed in the 
previous chapter, theories are powerful frameworks for explaining 
observations, and for making new predictions about the natural world. The 
theory of evolution is no exception. It is important to understand (see myth 
#2 in the list above) that evolution is an observable fact, and that 
evolutionary theory (which is not the same thing) is the best current 
explanation for those observable facts. Indeed, it is the most powerful 
explanatory framework in biology today. Theodosius Dobzhansky, a famous 
biologist, expressed this sentiment quite well when he wrote in 1973, 
“Nothing in biology makes sense except in the light of evolution.” On a 
daily basis, scientists around the world are using the theory of evolution to 
generate hypotheses, to interpret conclusions, and to make contributions to 
scientific knowledge. So let’s look at that powerful explanation in more 
detail. 


At its simplest, evolution is defined as “descent with modification”. That is 
joined to another concept, natural selection, to give us the first expression 
of the theory of evolution, published by Charles Darwin in 1859. Darwin’s 
genius was in recognizing, and thoroughly explaining, that descent with 
modification was a common phenomenon, and that selection, whether 
natural or artificial (e.g. animal breeding) was an explanation for life’s 


diversity. So let’s look more closely at natural selection, since Darwin 
identified it as the engine that drives the process of evolution. 


Natural selection (aka adaptive evolution) is, as Darwin pointed out 150+ 
years ago, analogous to the process by which animal breeders produce 
animals with novel traits (aka artificial selection). For example, a pigeon 
breeder might notice that one of his pigeons has an unusually large ruff of 
feathers around its neck. He breeds this pigeon with another pigeon, and 
selects the pigeons with the biggest ruffs from among the offspring to be the 
parents of the next generation. After a few cycles of this, some of the 
pigeon offspring will have very unusual and pronounced neck ruffs, and 
will look nothing at all like the original pigeon ancestor in that regard 
(figure 1, below). This common practice gets its name from the fact that the 
breeder selects, or chooses, specific animals to be the parents of the next 
generation. And it works; there are many examples where substantial 
changes in animal appearance, or behavior, can be brought about in just a 
few generations by applying this artificial method of selection. 


Darwin's pigeons (Original line drawings from Darwin's 
"Variation in Animals and Plants under Domestication", 1868). 
The common ancestor for all of these fancy pigeons was the Rock 
Pigeon (center). By selecting for unusual morphological 
characteristics, pigeon breeders are able to develop all of these 
unusual pigeons, and many more. 


Darwin’s genius, and the source of Huxley’s self-disparaging statement at 
the top of this chapter, was to recognize that this process could also occur in 
the absence of an individual who did the selecting. Natural selection, the 
idea for which Darwin is so famous, simply recognizes three well-known 
observations and puts them into a context that generates evolutionary 
change. Let’s look briefly at each of these three observations. 


The first thing that Darwin postulated is that the variations seen in living 
things are due, to a greater or lesser degree, to heritable factors. In other 
words, there are heritable variations among the individuals in a population 
of organisms. Let’s break down that term a bit, and look at each of the 
words, using examples mostly from human populations. 


Firstly, we know that there are variations among individuals in a 
population. Look around your classroom, or at your family picture album. 
You probably don’t look exactly like your brother or sister, and your mom 
and dad don’t look exactly like your uncles or aunts. So even in situations 
where the parents are the same, variation occurs among the offspring. 
Variation is even greater in a population of individuals who don’t share the 
same parents. Variation is normal, and easily observed. 


What about that other word, heritable? Again we now know that many of 
those variable traits are heritable, i.e. they are passed from one generation to 
the next. In humans, eye color, hair color, height, etc. are all characteristics 
that might be the same in you and your parents. If you have a dog or cat, 
and that dog or cat has offspring, you can often see aspects of the offspring 
(e.g. coat color, size) that are identical to those in the parental animal. One 
likely explanation for that observation is that you and your parents have 
some shared molecule or molecules that determine each of those traits. We 
now know (but Darwin didn’t) that the molecule is DNA, about which you 
will learn more later. On the other hand, some conditions are not heritable. 
For example, if you have a cat that lost its tail in a horrible and noisy 
accident involving a rocking chair and your 300-lb great-aunt, and if the cat 
has kittens, those kittens will have normal tails. The rocking chair might 
damage the cat’s tail, but not its DNA. At the time of Darwin, the 
mechanisms of heritability were not known (he knew nothing about genes), 
but everyone understood that some traits were heritable, and others were 
not. So again, the heritable variation that is necessary for evolution to occur 
is easily observed in the natural world. 


The second thing that Darwin observed, and that was a huge factor in his 
synthesis of these observations into his theory, is that not all of the 
individuals in a given generation will survive and reproduce to the same 
degree. Simple mathematics corroborates that. If all of the fruit flies from a 


single pair of fruit flies survived and produced a maximal number of 
offspring, after a mere 25 generations (which can take just a single year in 
this species) that population of flies would fill a ball 96 million miles in 
diameter, or more than the distance from the earth to the sun. Fruit flies 
have been around for lots longer than a year, and you can still see the sun, 
so obviously fruit flies do not all survive and reproduce. 


Finally, the third condition necessitates that these heritable variations can 
result in differences in survival or reproductive success. Again, there is 
abundant evidence for that. Inherited human conditions that result in mental 
retardation, or physical deformation, often mean that the affected individual 
will not survive or reproduce. Medical intervention has, in some cases, been 
able to counteract those disabilities and allow individuals with some 
inherited conditions to survive and reproduce, but in previous generations, 
or in populations of organisms that do not have access to medical care, 
many heritable variations were not represented in the next generation 
because the individuals with those variations simply did not reproduce. 


So the model Darwin proposed is quite simple. If all of those conditions 
were true, organisms with heritable variations that enhanced their chances 
for survival and reproduction would be more likely to be among the parents 
of the next generation, and the frequency of those organisms with those 
particular heritable variations would increase in the next generation. This is 
a simple idea, but it has many ramifications for the study of biology. 


It seems clear, just from observations we all have made, that these three 
conditions do pertain in the natural world. If that is the case, then the 
process of natural selection could operate, and variations that resulted in 
reproductive success would become more common in the population. It is 
important to understand that this process is the result of an interaction 
between the organisms and their environment. Over time, organisms that fit 
better into that environment will become more abundant in the population, 
and may eventually be the only organisms in the population. The term 
fitness, in this context, simply is a measure of how well individuals with 
certain traits survive and reproduce in a particular environment. The 
environment is an incredibly important aspect of this process. If the 
environment changes, organisms which were fit for the previous 


environment may suddenly find themselves less well-adapted, and rare 
organisms that were ill-adapted in the previous environment may suddenly 
become more fit to that new environment. Fitness is relative, and the 
environment is a major player in the determination of fitness. 


In addition, consideration of these processes in the real world leads to a 
better understanding of the questions in the introduction to this chapter. As 
you can see, the process of evolution is NOT random; the interaction of the 
organism and its environment leads to selection, and selection, by the very 
nature of the word, is not random. Just as an animal breeder chooses 
specific individuals as the parents of the next generation, the process of 
natural selection chooses specific individuals as the parents of the next 
generation, leading to evolution of the population. There are some 
important differences, however. In artificial selection, the breeder has a goal 
(e.g. to get a goat that produces more milk), and designs the breeding 
program with that goal in mind. In natural selection, there is no ultimate 
goal, and no plan; organisms are selected for their adaptation in a particular 
environment, which can (and often does) change. The process is unguided, 
in the sense that there is no goal in mind, but unguided is not the same thing 
as random. 


Secondly, careful consideration of this process also disproves the notion 
that evolution equals progress toward a “better” organism. An organism that 
is better adapted to one environment can be very ill-adapted if the 
environment changes. In that situation, a “worse” organism, one that is rare 
in the first environment, is now the “better” one in the new environment. 
That is not progress, it is just change. In fact, some organisms become so 
well-adapted to their environments that they lose some of the complex 
structures or pathways that their ancestors had. Cave fish have no eyes, 
even though their ancestors did. Whales have no legs, even though their 
ancestors did. These highly-adapted organisms are actually less complex 
than the ancestors from which they evolved. Evolution clearly is not a 
synonym for progress! 


Finally, it should be clear that evolution is a change at the level of the 
population, and not at the level of the organism. Natural selection acts on 
organisms, but the result of selection is seen in the next generation. And this 


change is usually very gradual; there is no need to invoke absurd situations 
where a Cat gives birth to a dog, or vice-versa. 


Darwin correctly pointed out the analogies between this process of natural 
selection and artificial selection, the well-known process that animal 
breeders used to select for interesting or useful variants in animal species. 
In other words, natural processes can generate the diversity we find in the 
natural world if all of those conditions are true, and if there is sufficient 
time to produce many generations. You will learn more in the studio 
exercises about how even small differences in reproductive success can, 
over time, lead to large changes in the characteristics of organisms in a 
population. Small changes (one or two genes in organisms that still are 
members of the same species) are sometimes described as micro-evolution. 
Larger changes that result in different species, for example, are described as 
macro-evolution. This is an artificial distinction, actually. Macro-evolution 
is merely micro-evolution that has proceeded for a longer time. For a clever 
graphical illustration of that, see figure 2 below. 


We all can agree (save for the severely color blind) that this text is red. 
We can also similarly agree that this text is blue. 


If we have red text and decide to change it by just a small amount, the change might be barely noticeable, but still a 
very small change. This, we will call our micro-evolution. Every word up to now can be considered red, with very 
minute changes in the hue. If I keep typing long enough, would anyone be able to tell me, just by looking, at which 
word or letter is this post no longer red, but actually purple or blue? All this micro-evolution keeps occurring in the 
text, with it's tiny changes in hue, but ultimately, I end up with a completely different color. It's actually the difference 
between what one would consider red and what one would consider purple (or a whole new species, in this analogy) 
which is macro-evolution. See, the common misunderstanding is, that macro-evolution means a dog being a direct 
offspring of some other different canine-like species, or even more stupidly, a cat coming from a dog. Well, that's not 
what macro-evolution is. There is really only one distinction between micro-evolution and macro-evolution, and it's 
the same distinction between their prefixes: micro and macro. Just like if something is microscopic or if something is 
macroscopic. Microscopic usually requires a microscope to see it because it's so small, but the macroscopic are things 
large enough to be seen by the common human eye. However, things of both size are completely visible and plainly 
exist, and there are many things in this universe between both general sizes. So as you read this, can you tell me the 
first word here that is blue, and not purple? After all, every change in color since the first word in this paragraph has 
only micro-evolved from the color next to it, but we've managed to macro-evolve through 2 colors. This, hopefully, 
will illustrate how it's illogical to believe that macro-evolution doesn't happen, even given time for enough micro- 
evolution to occur. 


So tell me -- what was the first purple word in the block of text above? What's the first blue word? Remember, if 
macro-evolution simply can not happen then you're saying the words you are reading now are still red. 


How very gradual changes can, over time, result in significant 
changes: A textual example. 


In summary, natural selection is a powerful agent, and recognition of this 
process was a powerful insight. Darwin proposed his theory in 1859, and 
elaborated on it in other books and other editions of the Origin of Species. 
Since Darwin’s time, other scientists have identified other agents, in 
addition to natural selection, that result in changes in the characteristics of a 
population, and you will learn more about those in later chapters. 
Additionally, other scientists made many predictions based on this 
explanatory framework, and did many experiments to test those predictions. 
Scientists are still engaged in that process today, and Darwin’s ideas have 
been confirmed many times over, and even extended so that we understand 
how the process works in much more detail than Darwin did. That is, as you 
learned in the previous chapter, one hallmark of a great theory. 


Evidence for Evolution 


There are multiple lines of evidence, many of which were unimagined in 
the time of Darwin, that support his explanation for the diversity of life. The 
following is not meant to be an exhaustive cataloguing of that evidence. 
Indeed, more evidence accumulates every day, making it impossible to 
point out all of the threads in that fabric. It is also important to recognize 
that the evidence doesn’t come just from biology. For example, as noted 
above, Darwin’s explanation would require a lot of time and many 
generations. If the earth was too young, none of this could have happened. 
The sciences of physics and geology confirm that the earth is over 4.5 
billion years old, which is plenty long enough for evolution to occur. The 
fossil record, the research subject of geology and paleontology, also 
provides substantial supporting evidence for Darwin’s big idea. The 
discovery of continental drift, and the development of plate tectonic theory, 
made sense of a lot of observations about both the fossil record and about 
populations of living organisms. Let’s look at a few of the lines of evidence, 
and see how they all weave together to make the coherent and elegant fabric 
that is the hallmark of a good scientific theory. 


The fossil record 


In science, radically new explanations can only be successful when the 
conventional explanations no longer explain all the observations. In the 
history of biology, this was the situation in the early part of the nineteenth 
century, when many interesting fossils were being discovered and carefully 
scrutinized. It soon became apparent that fossils were indeed the remains of 
once-living organisms, and that fossils in geologically younger strata 
seemed to be both similar and different from those in older strata. The fossil 
record showed that whole groups of organisms appeared and disappeared 
during the history of the earth. Others seemed to be much the same in rocks 
of different ages. Familiar organisms, particularly marine mollusks such as 
clams and snails, could be found in older rocks, but in many cases these 
organisms were not identical to the current organisms. Plant fossils told the 
same story. The reigning explanation for the diversity of life, creation of all 
these creatures at the same time and place, clearly did not explain these new 
observations. Evolutionary theory was a much more satisfying scientific 
explanation, and the development of that theory by Darwin and others 
started at that time. 


Since Darwin’s time the fossil record has become much more extensive, 
and the evidence for this explanation has become much more well- 
supported. Gaps in the fossil record that were pointed out by Darwin’s 
contemporaries have been gradually filled in. Indeed, the sciences of 
geology and paleontology, in combination with biology, have allowed 
scientists to make predictions about where, exactly, particular fossils in 
particular gaps should be found. 


The most recent (and spectacular) example of this was the discovery of 
fossilized remains of a creature that bridges the gap between fish and 
amphibians, which the first four-legged creatures (aka tetrapods) to move 
onto land. The fossil record, coupled with genetic evidence from modern- 
day amphibians and fish, indicated that this transition to land occurred 
about 375-400 million years ago. But only fish fossils, or amphibian fossils, 
had ever been found. Logic dictates that there should be a transitional 
creature, or “missing link” in popular jargon, which had characteristics of 
both fish and amphibians. It was reasoned that creatures such as this, if they 
existed, would probably live in shallow areas at the edge of seas or bays. 
Geologists knew which particular rock formations resulted from those sort 


of environments of that age, and so expeditions were dispatched to search 
for such fossils in one of those geological formations. These rocks were 
deposited in warm shallow tropical seas 375 million years ago, but are now, 
as aresult of continental drift, located on Ellesmere Island in the Canadian 
Arctic. In 2004 fossils were found in those rocks that elegantly fit that 
prediction; the creature was named Tiktaalik roseae. (figure 3, below). The 
genus name for this “fishapod” comes from the name of a fish and was 
suggested by local Inuits on Ellesmere Island, and the specific epithet 
“roseae” honors an anonymous donor who helped fund these grueling 
expeditions to the high Arctic. Tiktaalik “fins” have basic wrist bones, but 
no digits, or fingers. It is truly a missing link, and its discovery stems 
directly from predictions made on the basis of previous scientific 
observations, in a classic example of the power of the explanatory 
framework known as the theory of evolution. Descriptions of the 
expeditions, and lots more about the incredible insights that have come 
from those fossils, can be found in a charming book called “Your Inner 
Fish”, written by Neil Shubin and published in 2008. 


“Fishapod” evolution (By Maija Karala (Own work) [CC-BY- 
SA-3.0], via Wikimedia Commons. A cladogram showing the 


evolution of tetrapods, using the best-known transitional fossils. 
From bottom to top: Eusthenopteron, Panderichthys, Tiktaalik, 
Acanthostega, Ichthyostega, Pederpes. 


Comparative anatomy and embryology 


At the same time that the fossil record was making some scientists scratch 
their heads and question the creation explanation for the diversity of life, 
other scientists were looking more closely at these fossils and at the bones 
of existing organisms. These comparative anatomists also made 
observations which were much more easily explained by the theory of 
evolution. The different bones in fossil skulls, for example, could be 
compared to the bones in modern skulls, allowing anatomists to discern that 
the fossil skulls and the modern skulls had remarkable similarities in the 
number and the position of the individual bones in the skull. Most of the 
bones in a fossil fish skull have counterparts not only in modern fish skulls, 
but in fossil and modern amphibian skulls, or fossil and modern reptile 
skulls, and even fossil and modern mammal skulls. Occasionally the fossil 
record shows us when a skull bone is added or one is lost, and also allows 
us to track progressive modifications in the positions of these bones on the 
skull surface. We can only understand these observations in the light of 
evolutionary theory — if we conclude that the bones reflect the fact that each 
kind of organism is descended from some other. Descent with modification 
is the most satisfying scientific explanation for these observations. 


The anatomy of modern organisms also reflects this common ancestry. The 
limbs of all tetrapods contain a similar number and arrangement of bones, 
even though the size and shape of the bones can vary greatly in different 
organisms. For example, the two bones in your forearm, the radius and the 
ulna, have counterparts in other mammals (figure 2.4), in reptiles, in birds, 
and even in fossil dinosaurs and pleisiosaurs . If all of these structures were 
specifically created for moving around in a different environment (e.g. 
water for the plesiosaur and air for the bird or bat), simple engineering 
principles would dictate that different structures would be more efficient in 


those different situations. Yet the same structures, endlessly modified, are 
found in all of them. The simplest explanation for this is that the organisms 
share a common ancestor where that structure originated, and evolutionary 
mechanisms resulted in the modifications in size and shape that we see 
today. This phenomenon is known as homology; structures are said to be 
homologous structures if they occupy similar positions and arise from a 
common ancestral structure. 


A B C D 


Homologous bones in the forelimbs of four vertebrates (By 
Petter Bockman, via Wikimedia Commons). A-human, B-dog, C- 
bird, D-whale. The various colors indicate bones of various groups 
(e.g. dark brown = bones of the fingers, yellw = bones of the wrist, 

red = ulna, beige = radius, and light brown = humerus). The 
various bones in the forelimbs of four vertebrates differ in size and 
shape, resulting in very different morphologies of the forelimbs of 
these organisms. But both the number of bones, and their position 

relative to each other, are quite similar, as is their embryological 


development. These homologous parts provided one of Darwin’s 
arguments in support of his theory of evolution. 


Even vertebrates who have lost these limbs in the course of evolution (e.g. 
snakes) had similar structures prior to that evolutionary change. Figure 
shows the fossilized remains of a creature (Tetrapodophis amplectus) that 
lived in what is now Brazil 120 million years ago. It had a snake-like body 
and may be the ancestor to all snakes, but it also had four small limbs. The 
forelimb shown in that figure clearly has the humerus, radius, ulna and hand 
bones that are found in modern vertebrates. 

Homologous forelimb bones in a fossil snake 


Forelimb of Tetrapodophis 
amplectus, a four-legged snake 
from the early Cretaceous (120 

million years ago). Hu = 
humerus, ra = radius, ul = ulna 
and man = manus (hand). 

Photo from Martil, D. et al, 

Science 349:416-19 (2015). 


Embryologists also made predictions based on this evolutionary 
explanation. They predicted that homologous bones would arise from 
similar structures during the development of the embryo. For example, the 
forearm bone that we call the radius, which looks radically different in the 
forearms of a bat or a human or a mouse or a bird, would come from similar 
structures in the embryos of bats, humans, mice or birds. Those predictions 
also were found to be correct. So homology argues strongly for an 
explanation that invokes descent with modification. 


In contrast, the wings of insects and the wings of bats or birds do not have 
similar structures, although they have similar functions (to propel the 
organism through the air). These structures are said to be analogous rather 
than homologous; they share a function but do not arise from a structure 
that is found in a common ancestor. Indeed, if organisms predominantly had 
analogous structures, which would be different engineering solutions to a 
common problem, that evidence would be more consistent with the 
explanation of independent creation of those organisms. But homologous 
structures seem to be the much more common observation, making descent 
with modification a much more scientifically satisfying explanation. 


Comparative biochemistry 


One of the biggest surprises of modern biology came from the field of 
science known as biochemistry. Once biochemists started to unravel the 
mysteries of metabolism, the unity of life on this planet became quite 
obvious. Creatures with incredibly different morphologies, habitats, and 
lifestyles all seem to have incredibly similar metabolic pathways. Bacteria, 
bonobos, bats and bananas all use a molecule known as ATP (adenosine 
triphosphate) to store and provide energy within their cells, for example. 
The metabolic pathway known as glycolysis, which you will learn about in 
subsequent chapters, is found in all the organisms on the planet, and the 
enzymes that are used in that pathway are quite similar in these diverse 
organisms. Again, this argues strongly for common ancestry, which is a 
strong prediction that arises from a “descent with modification” 
explanation. Once an ancient cell developed these metabolic pathways, 
there was no need to re-invent that wheel. It is somewhat ironic that some 


of the best evidence for a particular explanation for the diversity of life 
comes from the discovery of the unity of life at the molecular level. 


Genetics and genomics 


Besides ATP, another molecule common to all life forms on the planet is 
DNA (deoxyribonucleic acid). This molecule stores genetic information, so 
it is the molecule of heredity. Its role in heredity also means that it can be 
modified under some circumstances, thus giving rise to the variations 
described above. Darwin knew nothing about DNA when he proposed his 
theory in 1859; his ideas about mechanisms of heredity were, in fact, 
spectacularly wrong. But the discovery of the mechanisms of heredity, 
starting with Mendel in 1866, and extended by many others in the early part 
of the 20" century, made it possible to finally propose mechanisms by 
which heritable variations arise and are transmitted between generations. In 
fact, the first 4 decades of the 20" century were the years when the two 
seemingly unrelated fields of genetics and evolution were united. This Neo- 
Darwinian synthesis, starring Theodosius Dobzhansky, Ernst Mayr, and 
George Gaylord Simpson, resulted in modern evolutionary theory, and 
allowed scientists from both genetics and evolutionary backgrounds to work 
together to make and test predictions. 


The elucidation of the structure of DNA by Watson and Crick in 1953, 
followed soon by the breaking of the genetic code, provided even more 
evidence for descent with modification. DNA, as you will learn later, 
functions as a repository of information. In order for the information to be 
used to build a cell or an organism, it must be read and translated into 
different molecules. The processes, and the enzymes, that do this work of 
reading and translating are virtually identical in all living creatures on the 
planet. The genetic code was, perhaps prematurely, called the “universal” 
genetic code for precisely that reason; it is translated identically in almost 
all organisms that have been discovered to date. Once again, this is a strong 
argument for common ancestry and descent with modification. 


But the really impressive outcome of this fusion of molecular knowledge 
and organismal knowledge comes from the study of the structure of genes, 


and genomes, at a detailed level. Incredibly, scientists have discovered 
molecular fossils of a sort — stretches of DNA which are not used in modern 
organisms, but which remain in the genome as a record of functions in the 
past. For example, chickens don’t have teeth, but they have genes for tooth 
proteins, turned off long ago, still lurking in their genomes. Those genes 
can be turned on under the right conditions, producing toothy structures, 
which were last seen in dinosaurs, the extinct ancestors of modern chickens. 
There is no good explanation for these observations, other than descent with 
modification. Similarly, detailed analysis of the DNA of organisms, 
including now some long-dead organisms like mammoths and 
Neanderthals, allows scientists to test predictions about common ancestry, 
and gain insights into the course of evolutionary change in all organisms. In 
fact, evidence from analysis of DNA, and other molecules, has allowed us 
to fine-tune our hypotheses about ancestry and relationships throughout the 
biological world, as explained in the next chapter on Taxonomy and 
Phylogeny. 


Taxonomy and phylogeny 
An introduction to taxonomy and phylogeny 


Taxonomy and Phylogeny 


"Birds in a way resemble fishes. For birds have their wings in the upper part 
of their bodies, and fishes have two fins in the front part of their bodies. 
Birds have feet on their under part, and most fishes have a second pair of 
fins in their under part...”" — Aristotle (384-322 B.C), De Incessu 
Animalium. 


Introduction — Differences and Similarities 


Observations and speculations about the similarities and differences of the 
life forms around us clearly have a long history. Aristotle’s ancient musings 
about animals pre-date the concept of homologous and analogous 
structures, which we discussed in the last chapter, but his insights are 
accurate today. Aristotle was the first to write about his attempts to classify 
animals into groups, and his classification scheme was the standard for 
many centuries. Attempts to refine the classification of animals (and other 
living things) continue even today, as you will see. Those classification 
schemes, throughout the centuries, have used many different criteria for 
separating living things into different groups. “How is this thing different 
from this other thing?” has been the focus of many scientific endeavors. 
But, as Aristotle recognized in the passage above, it is just as important to 
ask about the similarities, and not just focus on the differences. 


We use the words taxonomy or systematics to describe the activity of 
classifying and naming living things. There are many ways to divide living 
things into groups; the ability to recognize and classify things is a deeply- 
seated and oft-used human activity. Some of these schemes are based on 
habitat, e.g. water-dwelling creatures vs. land-dwelling creatures or aerial- 
dwelling creatures. Others are based on internal characters. For example, 
Aristotle’s two most basic groups were those with blood and those without 
blood, a grouping scheme that coincidentally neatly separates most of the 
vertebrates from most of the invertebrates. But most schemes have been 
based on morphology, such as size, shape, number and proportion of 


appendages, etc. This sort of classification seems to be easy enough to do, 
but, as you will see later in this chapter, it can lead to some interesting 
mistakes. 


Finally, it is important to understand that all classification schemes should 
be viewed as simply being hypotheses. Like any hypothesis, a 
classification scheme should change, or even be discarded, if new 
observations contradict the predictions of the hypothesis. This leads to some 
frustration on the part of some students, because (again) they would like to 
have some certainty about what they are learning. But a science where 
everything is certain would be a dead and dusty science, which certainly 
doesn’t describe the state of taxonomy today, or tomorrow. 


A brief history of taxonomy 


Domain - Eukarya 
Kingdom - Animalia 
Phylum - Chordata 
Class - Aves 
Order - Accipitriformes 
Family - Accipitridae 
Genus - Haliaetus 
Species - leucocephalus 


Taxonomic information for the Bald Eagle 
(photo by D. A. Rintoul) 


After Aristotle, there was not a lot of progress in taxonomy for many 
centuries. In fact, there may have been negative progress for some of that 
time, as Aristotle’s system was brushed aside or forgotten. But in the 1700’s 
a Swedish biologist who went by the Latin name Carolus Linneaus 
developed a system of biological classification that still underlies the 


system used today. His big contribution to the discipline was to introduce 
the concept of using two names to describe the smallest unit of 
classification, the species. In the Linnean system, every organism has a 
unique “scientific name”, consisting of a specific epithet preceded by a 
name for the next highest level of classification, the genus (plural = genera). 
Higher levels of classification included, in order above the genus, family, 
order, class, phylum, and kingdom. Subsequently another top level, the 
domain, was added to this hierarchy, giving us the classification scheme 
shown above ((link]). This bald eagle has the scientific name Haliaetus 
leucocephalus. There are 7 other members of the genus Haliaetus. The 
genus is placed in the Family Accipitridae, in the Order Accipitriformes, in 
the class Aves, in the Phylum Chordata, in the Kingdom Animalia, and in 
the Domain Eukarya. Biologists refer to a group of organisms, at any level, 
as a taxon (shorthand for taxonomic unit, plural = taxa). Thus a species is a 
taxon, as is a Genus, or a Family, or an Order, etc. 


There are an estimated 8-9 millions species on our planet. Every organism 
that has been described fits somewhere in this classification scheme. You 
can explore this in much more detail at the Tree of Life website. There you 
will find information on the thousands of species that have been described 
and named, as well as their currently assigned place in the taxonomic 
scheme. It is also worth pointing out that the basic unit of this scheme, the 
species, is not a well-defined term at all. There are multiple definitions of 
species that you can find with just a minimal bit of effort, and none of them 
is entirely satisfactory. Just as we learned about the definition of life, it is 
sometimes difficult to pin down an exact point on a hierarchy. As you will 
see from the material below, the problems with a definition of species might 
be related to the fact that evolution is ongoing, and that some groups of 
organisms are at different points on an evolutionary path at the present time. 


However, if we ignore the vexing issue of figuring out a widely-accepted 
definition for “species”, it is clear that a system based on this unit has 
several advantages. One of the immediate advantages of the Linnean system 
was that it allowed biologists to bypass the often confusing different 
common names that are used in various parts of the world, or in various 
languages. For example, the animal that is known as a moose in North 
America is confusingly called an elk in Europe. But when you refer to this 


creature by its scientific name (Alces alces), there is no confusion. That is 
why scientific papers always include the two term scientific name for a 
species. The hierarchical nature of the Linnean scheme is also useful, 
allowing us to easily understand the levels of similarity at different levels in 
the scheme. For example, organisms in the same genus can be very similar 
to each other, and may even be difficult to tell apart unless you are an 
expert. The similarity becomes less apparent for higher taxa; the class Aves 
includes that Bald Eagle mentioned above as well as your pet parakeet, 
which may screech like an eagle, but which is otherwise not very similar to 
an eagle at all. 


The original Linnean taxonomy was based, as noted above, primarily on 
external morphology. It also relied on the obvious fact that organisms are 
related to each other in many ways, and that some seem more closely 
related than others. However, a system based solely on morphological 
similarities and differences can lead to some interesting classification 
errors. For example, Linneaus had one Phylum named Vermes (Latin for 
“worms”). This obsolete taxon included animals that we now classify with 
the mollusks, others that we now classify with the vertebrates, and still 
others that we now classify with crustaceans, as well as those that are still 
classified as worms. This reinforces two aspects of taxonomy that are 
important to remember. The first is that taxonomic classification schemes 
are merely hypotheses, and should be discarded or modified if newly 
obtained information is not consistent with that hypothesis. The second is 
that classification schemes based only on one type of information (in this 
case, external morphology) can be quite mistaken. Using more than one 
type of information will lead to better and more stable taxonomies. 


Prior to Darwin’s time, classification was merely cataloging, and the 
cataloging system used morphology as the key characteristic for 
determining relationships. There is no theoretical basis for preferring one 
morphological cataloging scheme over another, however. The concept of 
evolution, and its prediction of common descent, provided that theoretical 
basis. Relationships, based on common ancestry, should provide a more 
accurate taxonomy. Besides being similar in size or shape, two organisms 
that were most closely related should have a common ancestor in the more 
recent past than would be the case for two less closely related organisms. 


The evolutionary history of the taxa was valuable and necessary 
information in this approach. The word for the determination of the 
evolutionary history of a species or group of species is phylogenetics, and 
the hypothesized evolutionary history and relationships of a species or 
group of species is a phylogeny. It quickly became clear that a taxonomic 
scheme that reflected phylogeny would be better than the arbitrary 
morphology-based schemes of the past. However, at the time of Darwin, 
and for many years thereafter, it was not exactly easy to discern the 
evolutionary history of organisms. So the development of a true 
phylogenetic taxonomy took a long time to develop, and, indeed, it is still 
being developed. 


Taxonomy should reflect phylogeny 


MRCA —” 


A simple phylogenetic tree. MRCA = 
Most recent common ancestor 


The current approach to determining relationships between two (or more) 
groups of organisms is the construction of what are called phylogenetic 
trees. Phylogenetic trees are hypothesized reconstructions of evolutionary 
history. They depict arrays of extant (currently living) organisms at the tips 
of the branches, and branch points that indicate a common ancestor. ({link]). 
A, B, C, D, and E in this diagram are the species being considered. The 
vertical axis represents the passage of time. The branch points represent 


organisms that are putative common ancestors of the organisms on the 
branches above. In some cases these ancestors are known species from the 
fossil record. In most cases they are not. A common ancestor for all of these 
organisms is the branch point above the root of the tree, known as the most 
recent common ancestor (MRCA). These trees can be horizontal and 
vertical arrangements, or diagonal arrangements, both of which are shown 
here. The two arrangements, in this case, represent identical trees in terms 
of the hypothesized relationships of species A, B, C, D, and E. 


Another critical point about these trees is that if you rotate the structures, 
using one of the branch points as a pivot, you don’t change the 
relationships. So just like the two trees above, which show the same 
relationships even though they are formatted differently, all of the trees in 
Figure 4.3 ((link]) are essentially identical in terms of depicting the 
relationships between the species A, B, C, and D. If you don’t see how that 
is true, just concentrate on the relationships and the branch points rather 
than on the sequence of species (A,B, C and D) shown across the tops of 
these diagrams. That sequence is not important; the branch structure 
underlying the sequence is what you will need to focus on. 


ABDC ACDB BCDA CODBA 


ir Ly ie 


ABDC ACDB BCDA CODBA 


YYW Y¥ 


Different depictions of the same 
phylogenetic tree. All of these 
depict the same relationships 

between the organisms A, B, C and 
D, 


To generate these tree structures, taxonomists use multiple characteristics to 
compare organisms, including external morphology, internal anatomy, 
behaviors, biochemical pathways, etc. Aristotle and Linneaus relied 
primarily on morphological characters (size and shape). However, as noted 
above, taxonomic schemes derived from comparing only a few 
characteristic can be very flawed. So modern taxonomists rely, if possible, 
on many characters, and taxonomies are constantly revised if additional 
characters are measured and included in the analysis. In addition, the 
development of a method called cladistics has revolutionized taxonomic 
thinking, and cladistics also depends on an understanding of evolutionary 
relationships. A clade is a group of organisms that consists of a common 
ancestor and all of its descendants. So another name for clade is a 
monophyletic group. For example, birds (including the bald eagle and your 
parakeet AND their ancestral organisms including one class of dinosaurs) 
are a clade. Clades can contain any number of species, but that number 
must include all of the descendants and the common ancestor. In the 
example above, A, B, C, D and E, as well as the ancestors indicated by the 
branch points, are a clade. A and B, plus their common ancestor, are also 
considered to be a clade. 


What's the difference between a phylogeny, a phylogenetic tree, and a 
cladogram? For our purposes, there really isn't much of a difference. In this 
class we will use these terms interchangeably — they all describe a tree 
structure that represents the hypothesized evolutionary relationships within 
a group of organisms, based on data derived from various sources. The 
important things to remember are 1) organisms are related, and 2) that we 
can represent our hypotheses about these relationships with tree structures. 


Cladistics relies on classifying characteristics of organisms as either 
ancestral or derived (another term that is sometimes used for ancestral 
characters is primitive). Ancestral characters are those inherited attributes 
that resemble those of an ancestor to the group. Derived characters are those 
features that are different from features found in the ancestor. The 
assumption of ancestral relationships in this approach is important, and 
signifies yet another way that evolutionary theory is the framework for 
understanding much of biology. 


But how do you know which features are ancestral, and which are derived? 
There are several ways to do that, but for your purposes, you can assume 
that characters shared by all the organisms in the group are probably 
ancestral. Other characters, not shared by all the organisms in the group, are 
assumed to be derived. Lists of characters are generated, and used to 
prepare a tree-like structure known as a cladogram. 


The best way to illustrate this process is with an example or two. Here is a 
table with some characters in rows and some organisms in columns. If there 
is an “X” in the column for an organism, the organism has that particular 
characteristic. 


List of characteristics of a group of 
animals that can be used to construct a 
cladogram. 


Which of these characters is common to all of these organisms? Obviously, 
it is the notochord. Assume that is the ancestral condition, and thus it should 
characterize the oldest ancestor at the base of any cladogram that you 
construct. Now you need to determine what the first branch in the tree is 
based on. That would be the character that is shared by all but one of these 
organisms, the presence of jaws. If you continue this process, adding a 
branch to the tree to depict groups that have, or do not have, a character, 
you will generate this cladogram ([link]). 


A cladogram constructed from the 
data in the table above. Using the 
character list in the table above, 
and recognizing that the notochord 
is common to all of these 
organisms, a cladogram was 
constructed, using the other 
characteristics in that list. Each 
shaded ellipse represents an 
ancestor possessing that trait, while 
the organism(s) on the opposite 
branch lack that trait. 


Now that you know how to construct one, there are a few other things about 
cladograms that you need to know. 


e The organisms along the top, or end, of a cladogram are not ordered in 
any particular way, and are not ancestors of each other. The order does 
not imply any sort of ranking from “primitive” to “advanced”. As 
discussed in the previous chapter, evolution is not synonymous with 
progress. As discussed above, the branches, and not the sequence of 
organisms across the top, are the important information in these 
diagrams. 


e The most closely related organisms have the most recent common 
ancestor, which is determined by counting the branch points backward 
from the organisms aligned across the top. For example , the bald 
Eagle and the Alligator have a more recent common ancestor than the 
Alligator and the Antelope; the Bald Eagle and the Alligator are more 
closely related than the Alligator and the Antelope. 

e The lines between branches represents the arrow of time, but in most 
cases the length of these lines is not directly related to the length of 
time involved between the branch points. Some representations of 
cladograms include an axis where time can be deduced, but if there is 
no such axis, do not assume that a longer line represents a longer 
length of time. 

e There are many ways to represent a cladogram, and many of these may 
look different, but will actually be identical. For example, the two 
cladograms shown in figure 4.2 depict the same set of relationships, 
even though one is vertically and horizontally aligned, and the other is 
diagonal in nature. In both cases organism C is more closely related to 
D (they share a relatively recent common ancestor) than A is related to 
B (which share a less recent common ancestor). 


Cladograms can be generated from any set of inherited characters. But they 
become powerful tools, both for understanding the world and for generating 
predictive hypotheses, when they include characters that we know are 
quantitatively representative of relatedness, such as amino acid or nucleic 
acid sequences. But the single most important character is one that most 
directly reflects the degree of common ancestry — the DNA sequence. Since 
(as you will learn in detail later) DNA is the molecule of “descent with 
modification”, similarities and differences in DNA sequences from different 
organisms are thus very useful in determining phylogenetic relationships. 
The development of DNA sequencing technology has allowed scientists to 
apply this tool to taxonomy, and this has resulted in an explosion of new 
and exciting discoveries about phylogeny. 


Morphological traits, such as those used to construct the cladogram above, 
can be preserved in the fossil record, but DNA generally is not preserved. 

However, since we know that your DNA was inherited from your parents, 
and your grandparents, etc., we can predict that DNA sequences from 


related individuals would contain evidence of that relatedness. These sorts 
of “molecular fossils” can be used to produce and refine cladograms, 
generating the structures we know as phylogenetic trees. 


“This view of life” 


It is important to also understand that phylogenetic trees are nested 
hierarchies, i.e., any individual set of branches is also part of a larger set of 
branches. This is easily seen in the accompanying figure ({link]). The clade 
containing the eagle and the alligator nests within a clade that also contains 
the antelope, and that clade nests within another clade, and another, etc. The 
hypothesis of descent with modification (i.e. evolution) absolutely predicts 
that the evolutionary history of organisms would be represented by a set of 
nested hierarchies. Cladistic analyses, particularly those based on DNA 
sequences, give results consistent with this prediction of Darwin’s theory. 


Cladogram showing the nested 
hierarchical arrangement of organisms 
predicted by Darwin's theory of 
evolution. 


If we continue backward in time from any tip of any branch of the 
phylogenetic tree above, we soon realize that all of these clades have a 
common ancestor at some point in the distant past. DNA evidence supports 
and strengthens this interpretation. As a matter of fact, the observation that 
all life forms on the planet have DNA as their genetic material is further 
support of this interpretation. The details of the arrangements of the various 
branches may change, as new observations are included in the analyses of 
relationships. The figure below ([link]) shows various phylogenetic trees 
that have been used in the past. Note that the fundamental conclusion, that 
all life on this planet came from a common ancestor, is a constant feature of 
all of these trees. Indeed, as new observations are made, particularly in the 
realm of DNA sequence data, this conclusion has become increasingly well- 
supported. 


Various depictions of the Tree of Life. 
These hypothesized trees reflect the state 
of knowledge at various times in the past. 

As new observations are made, new 


phylogenetic trees are constructed to 
accommodate that new knowledge. It is 
clear, from this example alone, that 
scientific hypotheses change in response 
to new discoveries and new knowledge. 
The currently accepted Tree of Life [link] 
will undoubtedly be modified in response 
to new scientific discoveries in the future. 


ARCHAEA - Color-enhanced scanning 
electron micrograph of Pyrococcus furiosus, 
Archaea are unicellular, do not have a cellular 


nucleus, and can be heterotrophic or PROTIST (ciliate)-A composite of images FUNGI -A fruiting body (mushroom) of a ANIMAL -A Prothonotary Warbler 


autotrophic. They are distinguished from of Stentor roeseli, Protists can be unicellular fungus in the Amazonian rainforest. Fungi (Protonotaria citrea) near Manhattan, 
bacteria by a variety of characteristics, or multicellular, do have a cellular nucleus, can be unicellular or multicellular, do have KS. Animals are multicellular, nucleated, 
including unique membrane lipids. and can be heterotrophic or autotrophic. a cellular nucleus, and are heterotrophic. and are heterotrophic. 


Tree of Life 


Bacteria Archaea Eukarya 
Green 
Filamentous Myxomycota 
Spirochetes Bacteria Entamoebae Animals 


Gram 
positives 


Methanosarcina 


Methanobacterium Halophiles 


Proteobacteria 


Methanococcus 


Planctomyces 


Bacteroides 
Cytophaga 


Tricomonads 


Microsporidia 
| Thermotoga 


Diplomonads 


PLANT - Leavenworth’s Eryngo (Eryngium 
leavenworthii) in the K-State University 
Gardens. Plants are multicellular, nucleated, 
and autotrophic. 


in patient cerebrospinal fluid. Bacteria are 
unicellular, do not have a cellular nucleus. 
and can be heterotrophic or autotrophic. 


The Tree of Life. The currently accepted hypothetical relationships 
between the three domains of living things. Bacteria, Archaea, and 


Eukarya (eukaryotes like you and me) are all thought to be descended 
from a common ancestor that lived billions of years ago. Image 
credits: Anthrax bacteria, from John A. Jernigan et al, "Bioterrorism- 
Related Inhalational Anthrax: The First 10 Cases Reported in the 
United States". Emerging Infectious Diseases 7(6), December 2001. 
Pyrococcus furiosus, from Wikimedia Commons. By Fulvio314 (Own 
work) (http://creativecommons.org/licenses/by-sa/3.0) Stentor, 
copyright-free image from the Protist Image Database. Mushroom, 
warbler, and eryngo are used with permission of the photographer, 
David A. Rintoul. 


The most widely accepted scheme has all living forms divided into three 
major Domains, Bacteria, Archaea, and Eukarya. The evolutionary 
relationship between these largest taxa is shown above ([link]). Note that 
current data support the idea that the Eukarya (including me and you) are 
more closely related to the Archaea than they are to the Bacteria; Archaea 
and Eukarya have a more recent common ancestor compared to Bacteria 
and Eukarya. Each of these Domains can be further subdivided into 
Kingdoms, Phyla, Classes, Orders, Families, Genera, and Species. For 
example, humans (Homo sapiens) are in the Domain Eukarya, Kingdom 
Animalia, Phylum Chordata, Class Mammalia, Order Primates, Family 
Hominidae, Genus Homo, and Species sapiens. In some cases these 
classifications are further organized into taxa such as Superfamily, or 
divided into taxa such as Suborder, but those are details that need not 
concern us here. 


Indeed, the entire Tree of Life is a nested hierarchy. We’re all related. 
Darwin suspected this, and his theory predicted the phylogenetic trees that 
scientists have generated from the observations and other data available to 
us. In one of the most often-quoted passages from the Origin, he 
demonstrates the sense of wonder that all biologists have when 
contemplating the diversity of living forms. 


"There is grandeur in this view of life, with its several powers, having been 
originally breathed into a few forms or into one; and that, whilst this planet 


has gone cycling on according to the fixed law of gravity, from so simple a 
beginning endless forms most beautiful and most wonderful have been, and 
are being, evolved." - Charles Darwin, 1859. 


The Scope of Ecology 


Introduction 

""Ecology is the entire science of the relations of the organism to the 
surrounding exterior world, to which relations we can count on the broader 
sense all of the conditions of existence. These are partly of organic, partly 
of inorganic nature... It is the "household' of nature."" - Ernst Haeckel, 
1869, inventing and defining the word "ecology". 


Ecology is the study of the interactions of living organisms with their 
environment. The Greek root of the word, and the basis for Haeckel's 
analogy above, is olKoc (oikos), which means house or dwelling-place. 
Ecology simply means "knowledge of the house". One core goal of ecology 
is to understand the distribution and abundance of living things in the 
physical environment. Attainment of this goal requires the integration of 
scientific disciplines inside and outside of biology, such as biochemistry, 
physiology, evolution, biodiversity, molecular biology, geology, and 
climatology. Some ecological research also applies aspects of chemistry and 
physics, and it frequently uses mathematical models. 


Levels of Ecological Study 


When a discipline such as biology is studied, it is often helpful to subdivide 
it into smaller, related areas. For instance, cell biologists interested in cell 
signaling need to understand the chemistry of the signaling molecules 
(which can be sugars, proteins, lipids, gases, or other compounds), as well 
as the result of cell signaling. Ecologists interested in the factors that 
influence the survival of an endangered species might use mathematical 
models to predict how current conservation efforts affect endangered 
organisms. To produce a sound set of management options, a conservation 
biologist needs to collect accurate data, including current population size, 
factors affecting reproduction (like physiology and behavior), habitat 
requirements (such as plants and soils), and potential human influences on 
the endangered population and its habitat (which might be derived through 
studies in sociology and urban ecology). Within the discipline of ecology, 
researchers work at four specific levels, sometimes discretely and 


sometimes with overlap: organism, population, community, and ecosystem 
((link]). 


Organisms, Populations, 
and Communities: Ina 
forest, each pine tree is an 
organism. Together, all the 
pine trees make up a 
population. All the plant and 
animal species in the forest 
comprise a community. 


Ecosystems: This coastal 
ecosystem in the 
southeastern United States 
includes living organisms 
and the environment in 
which they live. 


The Biosphere: 
Encompasses all the 
ecosystems on Earth. 


Ecologists study within several 
biological levels of 
organization. (credit 

“organisms”: modification of 
work by "Crystl"/Flickr; credit 

“ecosystems”: modification of 

work by Tom Carlisle, US Fish 
and Wildlife Service 
Headquarters; credit 
“biosphere”: NASA) 


Organismal Ecology 


Researchers studying ecology at the organismal level are interested in the 
adaptations that enable individuals to live in specific habitats. These 
adaptations can be morphological, physiological, and behavioral. For 
instance, the Karner blue butterfly (Lycaeides melissa samuelis) ({link]) is 
considered a specialist because the females preferentially oviposit (that is, 
lay eggs) on wild lupine. This preferential adaptation means that the Karner 
blue butterfly is highly dependent on the presence of wild lupine plants for 
its continued survival. 


The Karner blue butterfly 
(Lycaeides melissa samuelis) 
is a rare butterfly that lives 
only in open areas with few 
trees or shrubs, such as pine 
barrens and oak savannas. It 
can only lay its eggs on 
lupine plants. (credit: 
modification of work by J & 
K Hollingsworth, USFWS) 


After hatching, the larval caterpillars emerge and spend four to six weeks 
feeding solely on wild lupine ({link]). The caterpillars pupate (undergo 
metamorphosis) and emerge as butterflies after about four weeks. The adult 
butterflies feed on the nectar of flowers of wild lupine and other plant 


species. A researcher interested in studying Karner blue butterflies at the 
organismal level might, in addition to asking questions about egg laying, 
also ask questions about the butterflies’ preferred temperature (a 
physiological question), or the behavior of the caterpillars when they are at 
different larval stages (a behavioral question). 


The wild lupine 
(Lupinus 
perennis) is the 
host plant for the 
Karner blue 
butterfly. 


Population Ecology 


A population is a group of interbreeding organisms that are members of the 
same species living in the same area at the same time. A population is 
identified, in part, by where it lives, and the area it occupies, which may 


have natural or artificial boundaries. Natural boundaries might be rivers, 
mountains, or deserts, while examples of artificial boundaries include 
mowed grass, man-made structures, or roads. The study of population 
ecology focuses on the number of individuals in an area and asks how and 
why population size changes over time. Population ecologists are 
particularly interested in counting the Karner blue butterfly, for example, 
because it is classified as federally endangered. However, the distribution 
and density of this species is highly influenced by the distribution and 
abundance of wild lupine. Researchers might ask questions about the 
factors leading to the decline of wild lupine and how these affect Karner 
blue butterflies. For example, ecologists know that wild lupine thrives in 
open areas where trees and shrubs are largely absent. In natural settings, 
intermittent wildfires regularly remove trees and shrubs, helping to 
maintain the open areas that wild lupine requires. Mathematical models can 
be used to understand how wildfire suppression by humans has led to the 
decline of this important plant for the Karner blue butterfly. 


Community Ecology 


A biological community consists of the populations of all the species 
within an area, typically a three-dimensional space, and the interactions 
within and among these species. Community ecologists are interested in the 
processes driving these interactions and their consequences. Questions 
about intraspecific interactions (interactions between members of the 
Same species) often focus on competition among members of the same 
species for a limited resource. Ecologists also study interactions between 
members of different species; these are called interspecific interactions. 
Examples of interspecific interactions include predation, parasitism, 
herbivory, competition, and pollination. These interactions can have 
regulating effects on population sizes, and can impact the ecological and 
evolutionary processes, eventually affecting species diversity. 


For example, Karner blue butterfly larvae form mutualistic relationships 
with ants. Mutualism is a form of long-term relationship that has 
coevolved between two species and from which each species benefits. For 
mutualism to exist between individual organisms, each species must receive 
some benefit from the other as a consequence of the relationship. 


Researchers have shown that there is an increase in the probability of 
survival when Karner blue butterfly larvae (caterpillars) are tended by ants. 
This might be because the larvae spend less time in each life stage when 
tended by ants, which provides an advantage for the larvae. Meanwhile, the 
Karner blue butterfly larvae secrete a carbohydrate-rich substance that is an 
important energy source for the ants. Both the Karner blue larvae and the 
ants benefit from their interaction. 


Ecosystem Ecology 


Ecosystem ecology is an extension of organismal, population, and 
community ecology. The ecosystem is composed of all the biotic 
components (living things) in an area along with the abiotic components 
(non-living things) of that area; this definition hearkens back to Haeckel's 
original definition (above). Some of the abiotic components include air, 
water, and soil. Ecosystem biologists ask questions about how nutrients and 
energy are stored and how they move among organisms and the 
surrounding atmosphere, soil, and water. 


The Karner blue butterflies and wild lupine live in an oak-pine barren 
habitat. This habitat is characterized by natural disturbance and nutrient- 
poor soils that are low in nitrogen. The availability of nutrients is an 
important factor in the distribution of the plants that live in this habitat. 
Researchers interested in ecosystem ecology could ask questions about the 
importance of limited resources and the movement of resources, such as 
nutrients, through the biotic and abiotic portions of the ecosystem. 


Note: 

Career Connection 

Ecologist 

A career in ecology contributes to many facets of human society. 
Ecologists can conduct their research in the laboratory and outside in 
natural environments ([link]). These natural environments can be as close 
to home as the stream running through your campus or as far away as the 
hydrothermal vents at the bottom of the Pacific Ocean. Ecologists manage 


natural resources such as white-tailed deer populations (Odocoileus 
virginianus) for hunting or aspen (Populus spp.) timber stands for paper 
production. Ecologists also work as educators who teach children and 
adults at various institutions including universities, high schools, museums, 
and nature centers. Ecologists may also work in advisory positions 
assisting local, state, and federal policymakers to develop laws that are 
ecologically sound, or they may develop those policies and legislation 
themselves. To become an ecologist requires an undergraduate degree, 
usually in a natural science. The undergraduate degree is often followed by 
specialized training or an advanced degree, depending on the area of 
ecology selected. Ecologists should also have a broad background in the 
physical sciences, as well as a sound foundation in mathematics and 
Statistics. But even if you don't plan to become an ecologist, understanding 
ecological issues as a voter and citizen can help society meet the basic 
human needs of food, shelter, and health care. 


This landscape ecologist is releasing a black-footed ferret 
(shown at right) into its native habitat as part of a study. (credit - 
biologist photo: USFWS Mountain Prairie Region, NPS; black- 

footed ferret photo, David A. Rintoul) 


Ecology of Ecosystems 


Introduction 
"The early bird gets the worm, but the second mouse gets the cheese." 
Willie Nelson, American musician 


Competition for limited resources, whether it is a worm or a chunk of 
cheese, is an essential component of the evolutionary mechanism we call 
natural selection. Competition in communities (all living things within 
specific habitats) is observed both between members of the same species, 
and between members of different species. The resources for which 
organisms compete include food (or sunlight in the case of plants), mineral 
nutrients, nesting habitat, etc. Other critical factors influencing community 
dynamics are the components of its physical and geographic environment: a 
habitat’s latitude, amount of rainfall, topography (elevation), and 
temperature. These are all important environmental variables that help 
determine which organisms can exist within a particular area. 


An ecosystem is a community of living organisms and their interactions 
with their abiotic (non-living) environment. Ecosystems can be small, such 
as the tide pools found near the rocky shores of many oceans, or large, such 
as the Amazon Rainforest in Brazil ([link]). 


(a) (b) 


A (a) tidal pool ecosystem in Matinicus Island in 
Maine is a small ecosystem, while the (b) Amazon 
Rainforest in Brazil is a large ecosystem. (credit a: 

modification of work by “takomabibelot’”/Flickr; credit 
b: modification of work by Ivan Mlinaric) 


There are three broad categories of ecosystems based on their general 
environment: freshwater, ocean water, and terrestrial. Within these broad 
categories are individual ecosystem types based on the organisms present 
and the type of environmental habitat. 


Ocean ecosystems are the most common, covering 75 percent of the Earth's 
surface and consisting of two general types: shallow ocean (near islands and 
continents), and the deep ocean. The shallow ocean ecosystems include 
extremely biodiverse coral reef ecosystems. The surface water of the deep 
ocean is known for its large numbers of plankton (small organisms that 
disperse at the mercy of the winds and currents). Planktonic organisms can 
be phytoplankton (photosynthetic organisms), or zooplankton (tiny animals 
or animal larvae, which feed on the phytoplankton). These two 
environments are globally important; the phytoplankton perform 40 percent 
of all photosynthesis on the planet (i.e., produce 40% of the oxygen and fix 
40% of the CO>). Although not as diverse as the other two, deep ocean 
ecosystems contain a wide variety of marine organisms. Such ecosystems 
exist even at the bottom of the ocean where light is unable to penetrate. 


Freshwater ecosystems are the rarest, occurring on only 1.8 percent of the 
Earth's surface. Lakes, rivers, streams, and springs comprise these systems; 
they are quite diverse, and support a variety of fish, amphibians, reptiles, 
insects, phytoplankton, fungi, and bacteria. 


Terrestrial ecosystems, also known for their diversity, are grouped into large 
categories called biomes, such as tropical rain forests, savannas, deserts, 
coniferous forests, deciduous forests, and tundra. Grouping these 
ecosystems into just a few biome categories obscures the great diversity of 
the individual ecosystems within them. For example, there is great variation 
in desert biomes: the saguaro cacti and other plant life in the Sonoran 
Desert, in the United States and Mexico, are relatively abundant compared 
to the lack of plant life in the desolate rocky desert of Boa Vista, an island 
off the coast of Western Africa ([link]). 


(b) 


Desert ecosystems, like all ecosystems, can vary 
greatly. The desert in (a) Saguaro National Park, 
Arizona, has abundant plant life, while the rocky desert 
of (b) Boa Vista island, Cape Verde, Africa, is devoid 
of plant life. (credit a: modification of work by Jay 
Galvin; credit b: modification of work by Ingo 
Wolbern) 


Ecosystems are complex with many interacting parts, and dissecting the 
roles of these interacting components can be a challenge. Furthermore, 
ecosystems are routinely exposed to various disturbances, or changes in the 
environment that affect their compositions. For example, variations in 
rainfall and temperature can affect patterns and rates of plant growth, even 
though this may take several years. Many disturbances are a result of 
natural processes. For example, fire is a disturbance that can be caused by a 
lightning strike in a prairie or forest ecosystem. Recovery from disturbances 
can be highly variable as well; some ecosystems (e.g. prairie) are adapted to 
fire and can regenerate quickly. Others might recover more slowly. Other 
disturbances are the result of human activities. The impact of environmental 
disturbances caused by human activities is as important as the changes 
wrought by natural processes. Human agricultural practices, air pollution, 
acid rain, global deforestation, overfishing, eutrophication, oil spills, and 
illegal dumping on land and into the ocean are disturbances, and biological 
responses to these are of interest to ecologists and conservationists. 


Equilibrium is the steady state of an ecosystem where all organisms are in 
balance with their environment and with each other. In ecology, two 
parameters are used to measure changes in ecosystems: resistance and 
resilience. The ability of an ecosystem to remain at equilibrium in spite of 
disturbances is called resistance. The speed at which an ecosystem recovers 
equilibrium after being disturbed is its resilience. Ecosystem resistance and 
resilience are especially important when considering human impact. The 
nature of an ecosystem may change to such a degree that it can lose its 
resilience entirely. This process can lead to the complete destruction or 
irreversible altering of the ecosystem. 


Food Chains and Food Webs 


The term “food chain” is sometimes used metaphorically to describe human 
social situations. In this sense, food chains are thought of as a competition 
for survival, such as “who eats whom?” Someone eats and someone is 
eaten. Therefore, it is not surprising that in our competitive “dog-eat-dog” 
society, individuals who are considered successful are seen as being "at the 
top of the food chain", consuming all others for their benefit, whereas the 
less successful are seen as being at the bottom. 


The scientific understanding of a food chain is more precise than in its 
everyday usage. In ecology, a food chain is a linear sequence of organisms 
through which nutrients and energy pass: primary producers, primary 
consumers, and higher-level consumers are used to describe ecosystem 
structure and dynamics. There is a single path through the chain. Each 
organism in a food chain occupies what is called a trophic level (composed 
of organisms that share the same function in the food chain and the same 
nutritional relationship to the primary sources of energy). Depending on 
their role as producers or consumers, species or groups of species can be 
assigned to one or more trophic levels; for example bears eat plants (and 
thus are primary consumers) and also eat other animals (and thus are 
secondary or tertiary consumers). 


In many ecosystems, the bottom of the food chain consists of 
photosynthetic organisms (plants and/or phytoplankton), which are called 
primary producers. The organisms that consume the primary producers 


are herbivores: the primary consumers. Secondary consumers are usually 
carnivores that eat the primary consumers. Tertiary consumers are 
carnivores that eat other carnivores. Higher-level consumers feed on the 
next lower tropic levels, and so on, up to the organisms at the top of the 
food chain: the apex consumers. In the Lake Ontario food chain shown in 
[link], the Chinook salmon is the apex consumer at the top of this food 
chain. 


One of the classes of consumers deserves special mention; these are the 
decomposers, which break down waste or dead organic matter. Fungi and 
bacteria are decomposers in many ecosystems, utilizing the chemical energy 
in dead organic material to fuel their own metabolic processes. Some of the 
decomposers are also known as detritivores (literally, detritus- or debris- 
eaters). These are generally multicellular animals such as earthworms, 
crabs, slugs, vultures, etc. which not only feed on dead organic matter, but 
often fragment it as well, making it more available for bacterial or fungal 
decomposers. These organisms have a critical role in ecosystems, and are 
one of the main mechanisms by which nutrients get recycled for other 
organisms to use again. Even apex consumers such as the Chinook salmon 
have to die sometime, and the nutrients in their bodies can nourish a host of 
detritivores and decomposers. 


ORGANISM TROPHIC LEVEL 


pst 


ook salmon 


Slimy sculpin 


Mollusks 


tt 


Green algae 


These are the trophic levels 
of a food chain in Lake 
Ontario at the United States- 
Canada border. Energy and 
nutrients flow from 
photosynthetic green algae at 
the bottom to the top of the 
food chain: the introduced 
Chinook salmon. 


One major factor that limits the length of food chains is energy. 
Approximately 90% of the energy entering the system (from sunlight 
converted to carbohydrates by the primary producers) is lost as heat 
between one trophic level to the next, as explained by the second law of 
thermodynamics. Put another way, only 10% of the energy in a lower 
trophic level is transferred to the next trophic level. Thus, after a limited 
number of trophic levels (energy transfers), the amount of energy remaining 
in the food chain may not be great enough to support viable populations at 
yet a higher trophic level. 


The loss of energy between trophic levels is illustrated by the pioneering 
studies of Howard T. Odum in the Silver Springs, Florida, ecosystem in the 
1940s ([link]). The primary producers contained 20,819 kcal/m?/yr 
(kilocalories per square meter per year), the primary consumers contained 
3368 kcal/m?/yr, the secondary consumers contained 383 kcal/m?/yr, and 
the tertiary consumers only conained 21 kcal/m?/yr. Thus, there is little 
energy remaining for another level of consumers in this ecosystem. 


Tertiary consumers 
Secondary consumers 


Primary consumers 


Primary producers 


5,000 10,000 15,000 
Energy content (kcal/m2/yr) 


The relative energy in trophic levels in a Silver 
Springs, Florida, ecosystem is shown. Each 
trophic level has less energy available and 
supports fewer organisms at the next level. 


There is a one problem when using food chains to describe most 
ecosystems. Even when all organisms are grouped into appropriate trophic 
levels, some of these organisms can feed on species from more than one 
trophic level, as noted above. Likewise, some of these organisms can be 
eaten by species from multiple trophic levels. In other words, a strictly 
linear model of ecosystems, the food chain, does not completely describe 
ecosystem structure. A holistic model — which accounts for all the 
interactions between different species and their complex interconnected 
relationships with each other and with the environment — is a more 
accurate and descriptive model for ecosystems. We call such models food 
webs. A food web is a graphic representation of a holistic, non-linear web 
of primary producers, primary consumers, and higher-level consumers used 
to describe ecosystem structure and dynamics ([link]). 


This food web shows the interactions between organisms across 
trophic levels in the Lake Ontario ecosystem. Primary producers are 
outlined in green, primary consumers in orange, secondary consumers 
in blue, and tertiary consumers in purple. Arrows point from an 
organism that is consumed to the organism that consumes it. Notice 
how some lines point to more than one trophic level. For example, the 
opossum shrimp eats both primary producers and primary consumers. 
(credit. NOAA, GLERL) 


A comparison of the two types of structural ecosystem models reveals 
strengths for both models. Food chains are more flexible for analytical 
modeling, are easier to follow, and are easier to experiment with, whereas 
food web models more accurately represent ecosystem structure and 
dynamics, and data can be directly used as input for simulation modeling. 


Two general types of food webs are often shown interacting within a single 
ecosystem. A grazing food web (such as the Lake Ontario food web in 
[link]) has plants or other photosynthetic organisms at its base, followed by 
herbivores and various carnivores. A detrital food web consists of a base of 
organisms that feed on decaying organic matter (dead organisms), called 
decomposers or detritivores. These organisms are usually bacteria or fungi 
that recycle organic material back into the biotic part of the ecosystem as 
they themselves are consumed by other organisms. As all ecosystems 
require a method to recycle material from dead organisms, most grazing 
food webs have an associated detrital food web. For example, in a meadow 
ecosystem, plants may support a grazing food web of different organisms, 
primary and other levels of consumers, while at the same time supporting a 
detrital food web of bacteria, fungi, and detrivorous invertebrates feeding 
off dead plants and animals. 


Note: 

Evolution Connection 

Three-spined Stickleback 

It is well established that changes in the environment play a major role in 
the evolution of species within an ecosystem. However, little is known 
about how the evolution of species within an ecosystem can alter the 
ecosystem environment. In 2009, Dr. Luke Harmon, from the University of 
Idaho in Moscow, published a paper that for the first time showed that the 
evolution of organisms into subspecies can have direct effects on their 
ecosystem environment.!{2mote] 

Nature (Vol. 458, April 1, 2009) 


The three-spine stickleback (Gasterosteus aculeatus) is a freshwater fish 
that evolved from a saltwater fish. Evolutionary changes enabled it to live 
in freshwater lakes about 10,000 years ago, which is considered a recent 
development in evolutionary time ([link]). Over the last 10,000 years, these 
freshwater fish then became isolated from each other in different lakes. 
Depending on which lake population was studied, findings showed that 
these sticklebacks then either remained as one species or evolved into two 
species. The divergence of species occurred because different populations 
used different areas of the lake for feeding. 

Dr. Harmon and his team created artificial pond microcosms in 250-gallon 
tanks and added muck from freshwater ponds as a source of zooplankton 
and other invertebrates to sustain the fish. In different experimental tanks 
they introduced one species of stickleback from either a single-species or 
double-species lake. 

Over time, the team observed that some of the tanks bloomed with algae 
while others did not. This puzzled the scientists, and they decided to 
measure some water quality parameters, including the amount of dissolved 
organic carbon (DOC). DOC consists of organic compounds such as amino 
acids, carbohydrates, lignins, and many others; these are usually derived 
from decomposition of plant material in the water. DOC can vary not only 
in composition, but also in the size of the particles. Larger aggregates of 
decaying organic matter can give pond-water its slightly brownish color. It 
turned out that the water from the tanks with two-species fish contained 
larger particles of DOC (and hence darker water) than water with single- 
species fish. This increase in DOC blocked the sunlight and prevented 
algal blooming. Conversely, the water from the single-species tank 
contained smaller DOC particles, allowing more sunlight penetration to 
fuel the algal blooms. As the authors point out, "sticklebacks act as 
ecosystem engineers, strongly affecting the composition of the DOC pool 
and the physical light environment." 

This change in the environment, which is due to the different feeding 
habits of the stickleback species in each lake type, probably has a great 
impact on the survival of other species in these ecosystems, especially 
other photosynthetic organisms. Thus, the study shows that, at least in 
these ecosystems, the environment and the evolution of populations have 
reciprocal effects that may now be factored into simulation models. 


The three-spined stickleback 
evolved from a saltwater fish to 
freshwater fish. (credit: Barrett 

Paul, USFWS) 


The Laws of Thermodynamics 


Introduction 

"Nothing in life is certain except death, taxes and the second law of 
thermodynamics. All three are processes in which useful or accessible 
forms of some quantity, such as energy or money, are transformed into 
useless, inaccessible forms of the same quantity. That is not to say that these 
three processes don't have fringe benefits: taxes pay for roads and schools; 
the second law of thermodynamics drives cars, computers and metabolism; 
and death, at the very least, opens up tenured faculty positions." Seth Lloyd, 
Nature 430, 971 (26 August 2004) 


Thermodynamics refers to the study of energy and energy transfer 
involving physical matter. The matter and its environment relevant to a 
particular case of energy transfer are classified as a system, and everything 
outside of that system is called the surroundings. For instance, when heating 
a pot of water on the stove, the system includes the stove, the pot, and the 
water. Energy is transferred within the system (between the stove, pot, and 
water). There are two types of systems: open and closed. An open system is 
one in which energy can be transferred between the system and its 
surroundings. The stovetop system is open because heat can be lost into the 
air. A closed system is one that cannot transfer energy to its surroundings. 


Biological organisms are open systems. Energy is exchanged between 
them and their surroundings, as they consume energy-storing molecules and 
release energy to the environment by doing work. Like all things in the 
physical world, energy is subject to the laws of physics. The laws of 
thermodynamics govern the transfer of energy in and among all systems in 
the universe. 


The First Law of Thermodynamics 


The first law of thermodynamics deals with the total amount of energy in a 
system. It states that the total amount of energy in a closed system is 
constant. Energy exists in many different forms. According to the first law 
of thermodynamics, energy may be transferred from place to place or 
transformed into different forms within a system, but it cannot be created or 


destroyed. This is the principle of conservation of energy. Transfers and 
transformations of energy take place around us all the time. Light bulbs 
transform electrical energy into light energy. Gas stoves transform chemical 
energy from natural gas into heat energy. Plants perform one of the most 
biologically useful energy transformations on earth: that of converting the 
energy of sunlight into the chemical energy stored within organic 
molecules. Some examples of energy transformations are shown in [link]. 


The challenge for all living organisms is to obtain energy from their 
surroundings in forms that they can transfer or transform into usable energy 
to do work. Living cells have evolved to meet this challenge very well. 
Chemical energy stored within organic molecules such as sugars and fats is 
transformed through a series of cellular chemical reactions into energy 
within molecules of ATP. Energy in ATP molecules is easily accessible to 
do work. Examples of the types of work performed by cells include 
building complex molecules, transporting materials, powering the beating 
motion of cilia or flagella, contracting muscle fibers to create movement, 
and reproduction. 


Chemical energy Light energy 


>» > 


Kinetic energy Chemical energy 


Shown are two examples of 
energy being transferred from 
one system to another and 
transformed from one form to 
another. Humans can convert 
the chemical energy in food, 
like this ice cream cone, into 
kinetic energy (the energy of 
movement to ride a bicycle). 
Plants can convert 
electromagnetic radiation (light 
energy) from the sun into 
chemical energy. (credit “ice 
cream”: modification of work 
by D. Sharon Pruitt; credit “kids 
on bikes”: modification of work 
by Michelle Riggen-Ransom; 


credit “leaf”: modification of 
work by Cory Zanker) 


The Second Law of Thermodynamics 


A living cell’s primary tasks of obtaining, transforming, and using energy to 
do work may seem simple. However, the second law of thermodynamics 
explains why these tasks are harder than they appear. None of the energy 
transfers we’ve discussed is completely 100 percent efficient. In every 
energy transfer, some amount of energy is lost in a form that is unusable. In 
most cases, this form is heat energy. Thermodynamically, heat energy is 
defined as the energy transferred from one system to another that is not 
doing work. For example, when an airplane flies through the air, some of 
the energy of the flying plane is lost as heat energy due to friction with the 
surrounding air. This friction actually heats the air by temporarily 
increasing the speed of air molecules. Likewise, some energy is lost as heat 
energy during cellular metabolic reactions. This is good for warm-blooded 
creatures like us, because heat energy helps to maintain our body 
temperature. Strictly speaking, no energy transfer is completely efficient, 
because some energy is always lost in an unusable form. 


An important concept in physical systems is that of order and disorder (also 
known as randomness). The more energy that is lost by a system to its 
surroundings, the less ordered and more random the system is. Scientists 
refer to the measure of randomness or disorder within a system as entropy. 
High entropy is a state with high disorder and low energy. To better 
understand entropy, think of a student’s bedroom. If no energy or work were 
put into it, the room would quickly become messy. It would exist in a very 
disordered state, one of high entropy. Energy must be put into the system, in 
the form of the student doing work and putting everything away, in order to 
bring the room back to a state of cleanliness and order. This state is one of 
low entropy. Similarly, a car or house must be constantly maintained with 
work in order to keep it in an ordered state. Left alone, the entropy of the 
house or car gradually increases through rust and degradation. Molecules 
and chemical reactions have varying amounts of entropy as well. For 
example, as chemical reactions reach a state of equilibrium, entropy 


increases, and as molecules at a high concentration in one place diffuse and 
spread out, entropy also increases. 


Energy Flow 
"All flesh is grass." - Isaiah 40:6 


All living things require energy in one form or another. Energy is required 
by most complex metabolic pathways (often in the form of adenosine 
triphosphate, ATP), especially those responsible for building large 
molecules from smaller compounds, and life itself is an energy-driven 
process. Living organisms would not be able to assemble macromolecules 
(proteins, lipids, nucleic acids, and complex carbohydrates) without a 
constant energy input. And yes, Isaiah was correct; your flesh and all flesh 
originated in the green plants of this planet. 


It is important to understand how organisms acquire energy and how that 
energy is passed from one organism to another through food webs and their 
constituent food chains. Food webs illustrate how energy flows 
directionally through ecosystems, including how efficiently organisms 
acquire it, use it, and how much remains for use by other organisms of the 
food web. The transfer of energy from one trophic level to the next is an 
important concept when examining the effects of human disturbance on an 
ecosystem. 


How Organisms Acquire Energy in a Food Web 


Energy is acquired by living things in three ways: photosynthesis, 
chemosynthesis, and the consumption and digestion of other living or 
previously living organisms. Organisms using the first two methods are 
called autotrophs (auto=self, these organisms feed themselves). Those that 
rely on consumption of others are called heterotrophs (hetero=other, these 
organisms are fed by others). Photosynthetic autotrophs (photoautotrophs) 
use sunlight as an energy source, whereas chemosynthetic autotrophs 
(chemoautotrophs) use inorganic molecules as an energy source. 
Autotrophs are critical for all ecosystems. Without these organisms, energy 
would not be available to other living organisms and life itself would not be 
possible. 


Photoautotrophs, such as plants, algae, and photosynthetic bacteria, serve as 
the energy source for a majority of the world’s ecosystems. These 
ecosystems are often described by grazing food webs. Photoautotrophs 
harness the solar energy of the sun by converting it to chemical energy in 
the form of ATP (and NADP). The energy stored in ATP is used to 
synthesize complex organic molecules, such as glucose. 


Chemoautotrophs are primarily bacteria that are found in rare ecosystems 
where sunlight is not available, such as in those associated with dark caves 
or hydrothermal vents at the bottom of the ocean ({link]). Many 
chemoautotrophs in hydrothermal vents use hydrogen sulfide (HS) 
released from the vents as a source of chemical energy. This allows 
chemoautotrophs to synthesize complex organic molecules, such as glucose, 
for their own energy and in turn supplies energy to the rest of the 
ecosystem, making chemoautotrophs the primary producers of their 
ecosystem. 


Swimming shrimp, a few squat lobsters, 
and hundreds of vent mussels are seen at a 
hydrothermal vent at the bottom of the 
ocean. As no sunlight penetrates to this 
depth, the ecosystem is supported by 


chemoautotrophic bacteria and organic 
material that sinks from the ocean’s 
surface. This picture was taken in 2006 at 
the submerged NW Eifuku volcano off 
the coast of Japan by the National 
Oceanic and Atmospheric Administration 
(NOAA). The summit of this highly 
active volcano lies 1535 m below the 
surface. 


Productivity within Trophic Levels 


The general term "production" refers to the amount of new organic matter 
generated by photosynthesis. Biologists have found it useful to define and 
measure production more precisely. The total amount of solar energy 
captured by photosynthesis is gross primary productivity or GPP. 
Producers can use some of this energy for their own maintenance and 
metabolism, and also use some to produce organic compounds that they 
accumulate. This latter fraction is called net primary productivity or NPP. 
This is the only energy, contained in the biomass of the producers, that is 
available to all the heterotrophic organisms in that ecosystem. 


Studies on both natural and agricultural systems have shown that plants 
capture and convert about 1.3 - 1.6% of the solar energy that is available. 
They use about a quarter of that captured energy for their own metabolism 
and maintenance, leaving only about 1% of the solar energy as net primary 
productivity. The standard unit for measuring productivity is grams of 
biomass per square meter per year, but it is important to remember that this 
biomass is actually converted to energy by the heterotrophic organisms. 
Productivity in various ecosystems ranges from approximately 2,000 
g/m?/yr in tropical forests, salt marches, etc., to less than 100 g/m?/yr in 
some desert ecosystems. An example of gross primary productivity is 
shown in the compartment diagram of energy flow within the Silver Springs 
aquatic ecosystem ([link]). In this ecosystem, the total energy accumulated 


by the primary producers (gross primary productivity) was shown to be 
20,810 kcal/m?/yr. 


Trophic levels in an aquatic ecosystem 


Primary producers 
13,187 20,810 
7,618 4,250 


2,265 3,368 
1,103 720 


Secondary consumers 
272 383 


to decomposers 


Tertiary consumers 
16 21 


respiration + heat 


Total heat and respiration 
20,810 


Gross productivity 
Net productivity 


Trophic levels and 
energy flow in the 
Silver Spring ecosystem 


Modeling Ecosystems Energy Flow: Ecological Pyramids 


The structure of ecosystems can be visualized with ecological pyramids, 
which were first described by the pioneering studies of Charles Elton in the 
1920s. Ecological pyramids show the relative amounts of various 


parameters (such as number of organisms, energy, and biomass) across 
trophic levels. 


Pyramids of numbers can be either upright or inverted, depending on the 
ecosystem. As shown in [link], typical grassland during the summer has a 
base of many plants and the numbers of organisms decrease at each trophic 
level. However, during the summer in a temperate forest, the base of the 
pyramid consists of few trees compared with the number of primary 
consumers, mostly insects. Because trees are large, they have great 
photosynthetic capability, and dominate other plants in this ecosystem to 
obtain sunlight. Even in smaller numbers, primary producers in forests are 
still capable of supporting other trophic levels. 


Another way to visualize ecosystem structure is with pyramids of biomass. 
This pyramid measures the amount of energy converted into living tissue at 
the different trophic levels. Using the Silver Springs ecosystem example, 
these data exhibit an upright biomass pyramid ((link]), whereas the pyramid 
from the English Channel example is inverted. The plants (primary 
producers) of the Silver Springs ecosystem make up a large percentage of 
the biomass found there. However, the phytoplankton in the English 
Channel example make up less biomass than the primary consumers, the 
zooplankton. As with inverted pyramids of numbers, this inverted pyramid 
is not due to a lack of productivity from the primary producers, but results 
from the high turnover rate of the phytoplankton. The phytoplankton are 
consumed rapidly by the primary consumers, thus, minimizing their 
biomass at any particular point in time. However, phytoplankton reproduce 
quickly, thus they are able to support the rest of the ecosystem. 


Pyramid ecosystem modeling can also be used to show energy flow through 
the trophic levels. Notice that these numbers are the same as those used in 
the energy flow compartment diagram in (({link]). Pyramids of energy are 
always upright, and an ecosystem without sufficient primary productivity 
cannot be supported. All types of ecological pyramids are useful for 
characterizing ecosystem structure. However, in the study of energy flow 
through the ecosystem, pyramids of energy are the most consistent and 
representative models of ecosystem structure ({link]). 


Note: 
Ecological Pyramids 


A. Biomass (dry mass, g/m2) 


Silver Springs, Florida English Channel 
Fishes 5 
Decomposers Fishes 11 eee 
baal acerca Herbivorous insects. 4 
snails 37 ‘ Phytoplankton 


B. Number of individuals per 0.1 hectare 


Grassland (summer) Temperate forest (summer) 
1 Bird 


90,000 Predatory insects 


200,000 Herbivorous 
insects 


200 trees 


C. Energy (kcal/m2/yr) 


Silver Springs, Florida 


isl Tertiary (apex) consumer 


Secondary consumer 
Decomposers ] Eh 


(fungi, bacteria) 
5060 


Fishes 21 


Fishes 383 fa Primary consumer 


Insects, snails ° 
3368 ica Primary producer 


Ecological pyramids depict the (a) biomass, (b) number of 
organisms, and (c) energy in each trophic level. 


Consequences of Food Webs: Biological Magnification 


One of the most important environmental consequences of ecosystem 
dynamics is biological magnification. Biological magnification is the 
increasing concentration of persistent, toxic substances in organisms at 
higher trophic levels, from the primary producers to the apex consumers. 
Many substances have been shown to bioaccumulate, including the 
pesticide dichlorodiphenyltrichloroethane (DDT), which was first 
publicized in the 1960s bestseller, Silent Spring, by Rachel Carson. DDT 
was a commonly used pesticide before it became known that DDT and its 


metabolites persist in ecosystems and organisms, and these compounds can 
have harmful effects on many species in the higher trophic levels. In some 
aquatic ecosystems, organisms in higher trophic levels consume many 
individuals from the trophic level below. Small amounts of toxins in the 
water become increasingly concentrated (magnified) from lower trophic 
levels to higher trophic levels. So, DDT occurs in low concentrations in the 
water is acquired by the producers, then magnified in the primary 
consumers (small aquatic animals), then magnified again in the secondary 
consumers (fish), and again in higher consumers such as fish-eating birds 
(Ospreys, Pelicans, Bald Eagles). High levels of DDT metabolites cause the 
eggshells of birds to become thin and fragile; they often crack or break long 
before the baby bird hatches out. This effect resulted in significant declines 
in populations of fish-eating birds. The use of DDT was banned in the 
United States in the 1970s. 


Other substances that biomagnify are polychlorinated biphenyls (PCBs), 
which were used in coolant liquids in the United States until their use was 
banned in 1979, and heavy metals, such as mercury, lead, and cadmium. 
These substances were best studied in aquatic ecosystems, where fish 
species at different trophic levels accumulate toxic substances that are 
found in low concentrations in the primary producers. As illustrated in a 
study performed by the National Oceanic and Atmospheric Administration 
(NOAA) in the Saginaw Bay of Lake Huron ((link]), PCB concentrations 
increased from the ecosystem’s primary producers (phytoplankton) through 
the different trophic levels of fish species. The apex consumer (walleye) has 
more than four times the amount of PCBs per gram, compared to 
phytoplankton. Additionally, based on results from other studies, birds that 
eat these fish may have PCB levels at least one order of magnitude higher 
than those found in the lake fish. 


ee 
Rainbow Smelt / 


Yellow 
Perch 


Alewife a 


White Sucker 


Phytoplankton 


This chart shows the PCB 
concentrations found at the 
various trophic levels in the 

Saginaw Bay ecosystem of Lake 
Huron. Numbers on the x-axis 
reflect enrichment with heavy 

isotopes of nitrogen (1°N), which 
is a marker for increasing trophic 
level. Notice that the fish in the 
higher trophic levels accumulate 
more PCBs than those in lower 
trophic levels. (credit: Patricia Van 
Hoof, NOAA, GLERL) 


Other concerns have been raised by the accumulation of heavy metals, such 
as mercury and cadmium, in certain types of seafood. The United States 
Environmental Protection Agency (EPA) recommends that pregnant women 
and young children should not consume any top predator species such as 
swordfish, shark, king mackerel, or tilefish, because of their high mercury 
content. These individuals are advised to eat fish low in mercury: salmon, 
tilapia, shrimp, pollock, and catfish, which are lower on the trophic 


pyramids in their ecosystems. Biological magnification is a good example 
of how ecosystem dynamics can affect our everyday lives, even influencing 
the food we eat. 


Biogeochemical Cycles 


Energy flows, nutrients cycle 


"We are stardust, we are golden, we are billion year old carbon." - Joni 
Mitchell 


Indeed, the elements that make up our bodies, and those of every other 
living thing, were born in dying stars, billions of years ago. And energy 
from our own star, the Sun, is an important player in making those elements 
available to living organisms on this planet. Energy flows directionally 
through ecosystems, entering as sunlight (or inorganic molecules for 
chemoautotrophs) and leaving as heat during the many transfers between 
trophic levels. However, the matter that makes up living organisms 
(nutrients) is conserved and recycled. The five most common elements 
associated with organic molecules—carbon, nitrogen, hydrogen, oxygen, 
and phosphorus—take a variety of chemical forms and may exist for long 
periods in the atmosphere, on land, in water, or beneath the Earth’s surface. 
Geologic processes, such as weathering, erosion, water drainage, and the 
subduction of the continental plates, all play a role in this recycling of 
materials. Because geology and chemistry have major roles in the study of 
this process, the recycling of inorganic matter between living organisms and 
their environment is called a biogeochemical cycle. It is important to 
understand that energy, flowing through ecosystems, is also needed to drive 
biogeochemical cycles. 


This image illustrates the flow of energy and the cycling of nutrients. 
The dark green lines represent the movement of nutrients and the 
dashed lines represent the movement of energy. As you can see, 
nutrients remain within the system while energy enter via 
photosynthesis and leaves the system primarily as heat energy, a non- 
biolgically useful form of energy. Work by Eva Horne and Robert A. 
Bear 


Water contains hydrogen and oxygen, which are essential to all living 
processes. The hydrosphere is the area of the Earth where water movement 
and storage occurs: as liquid water on the surface and beneath the surface, 
or frozen (rivers, lakes, oceans, groundwater, polar ice caps, and glaciers), 
and as water vapor in the atmosphere. Carbon is found in all organic 
macromolecules and is an important constituent of fossil fuels. Nitrogen is a 


major component of nucleic acids and proteins and is critical to human 
agriculture. Phosphorus, a major component of nucleic acids (along with 
nitrogen), is also one of the main ingredients in artificial fertilizers used in 
agriculture. Sulfur, an element that is involved in the 3—D folding of 
proteins (as in disulfide binding), is released into the atmosphere by the 
burning of fossil fuels, such as coal. Cycling and recycling of these 
chemicals from the environment to organisms and back again is critically 
important to all living things. 


The cycling of these elements is interconnected. For example, the 
movement of water is critical for the leaching of nitrogen and phosphate 
into rivers, lakes, and oceans. Furthermore, the ocean itself is a major 
reservoir for carbon. Thus, mineral nutrients are cycled, either rapidly or 
slowly, through the entire biosphere, from one living organism to another, 
and between the biotic and abiotic world. 


The Water (Hydrologic) Cycle 


Water is the basis of all living processes. The human body is more than 1/2 
water and human cells are more than 70 percent water. Thus, most land 
animals need a supply of fresh water to survive. However, when examining 
the stores of water on Earth, 97.5 percent of it is non-potable salt water 
({link]). Of the remaining water, 99 percent is locked underground as water 
or as ice. Thus, less than 1 percent of fresh water is easily accessible from 
lakes and rivers. Many living things, such as plants, animals, and fungi, are 
dependent on the small amount of fresh surface water supply, a lack of 
which can have massive effects on ecosystem dynamics. Humans, of 
course, have developed technologies to increase water availability, such as 
digging wells to harvest groundwater, storing rainwater, and using 
desalination to obtain drinkable water from the ocean. Although this pursuit 
of drinkable water has been ongoing throughout human history, the supply 
of fresh water is still a major issue in modern times. 


Freshwater 2.5% 
(35,000,000 km?) 


Lakes and rivers 0.3% === 


Groundwater (soil moisture, swamp 
water, permafrost) 30.8% 


Glaciers and permanent snow cover 
68.9% 


Only 2.5 percent of water on Earth is fresh water, 
and less than 1 percent of fresh water is easily 
accessible to living things. 


Water cycling is extremely important to ecosystem dynamics. Water has a 
major influence on climate and, thus, on the environments of ecosystems. 
Most of the water on Earth is stored for long periods in the oceans, 
underground, and as ice. [link] illustrates the average time that an individual 
water molecule may spend in the Earth’s major water reservoirs. Residence 
time is a measure of the average time an individual water molecule stays in 
a particular reservoir. A large amount of the Earth’s water is locked in place 
in these reservoirs as ice, beneath the ground, and in the ocean, and, thus, is 
unavailable for short-term cycling (only surface water can evaporate). 


Average Residence Time for Water Molecules 


| Biospheric (in living organisms) 1 week 


| Atmospheric 1.5 weeks 


| Rivers 2 weeks 


| Soil moisture 2 weeks—1 year 
"Swamps 1-10 years 


“Lakes & reservoirs 10 years 


This graph shows the average 
residence time for water molecules 
in the Earth’s water reservoirs. 


There are various processes that occur during the cycling of water, shown in 
[link]. These processes include the following: 


e evaporation/sublimation 
¢ condensation/precipitation 
e subsurface water flow 

e surface runoff/snowmelt 

e streamflow 


The water cycle is driven by the sun’s energy as it warms the oceans and 
other surface waters. This leads to the evaporation (water to water vapor) of 
liquid surface water and the sublimation (ice to water vapor) of frozen 
water, which deposits large amounts of water vapor into the atmosphere. 
Over time, this water vapor condenses into clouds as liquid or frozen 
droplets and is eventually followed by precipitation (rain or snow), which 
returns water to the Earth’s surface. Rain eventually permeates into the 
ground, where it may evaporate again if it is near the surface, flow beneath 


the surface, or be stored for long periods. More easily observed is surface 
runoff: the flow of fresh water either from rain or melting ice. Runoff can 
then make its way through streams and lakes to the oceans or flow directly 
to the oceans themselves. 


Rain and surface runoff are major ways in which minerals, including 
carbon, nitrogen, phosphorus, and sulfur, are cycled from land to water. The 
environmental effects of runoff will be discussed later as these cycles are 
described. 


ne Water, Gycle 


Volcanic 


ste: i ns 
. Zi Water in the atmosphere 
7 yp Sublimation 


Evapodlis piration 5 
} Evaporation 


\ \ C . 
\ ka \ IN 
Infiltragdn S43 

\ \ XS 


Water from the land and oceans enters the atmosphere by 
evaporation or sublimation, where it condenses into clouds and 
falls as rain or snow. Precipitated water may enter freshwater 
bodies or infiltrate the soil. The cycle is complete when surface 
or groundwater reenters the ocean. (credit: modification of 
work by John M. Evans and Howard Perlman, USGS) 


The Carbon Cycle 


Carbon is the second most abundant element in living organisms. Carbon is 
present in all organic molecules, and its role in the structure of 
macromolecules is of primary importance to living organisms. Carbon 
compounds contain especially high energy, particularly those derived from 
fossilized organisms, mainly plants, which humans use as fuel. Since the 
1800s, the number of countries using massive amounts of fossil fuels has 
increased. Since the beginning of the Industrial Revolution, global demand 
for the Earth’s limited fossil fuel supplies has risen; therefore, the amount of 
carbon dioxide in our atmosphere has increased. This increase in carbon 
dioxide has been associated with climate change and other disturbances of 
the Earth’s ecosystems and is a major environmental concern worldwide. 
Thus, the “carbon footprint” is based on how much carbon dioxide is 
produced and how much fossil fuel countries consume. 


The carbon cycle is most easily studied as two interconnected sub-cycles: 
one dealing with rapid carbon exchange among living organisms and the 
other dealing with the long-term cycling of carbon through geologic 
processes. The entire carbon cycle is shown in [link]. 


he Garbon Gyele 


V 
Li > J 
"i ~ i i irati A 
Fossil ca¥bon..1 ., Microbial respiration . 
[| and decomposition 


Carbon dioxide gas exists in the atmosphere and is dissolved in 
water. Photosynthesis converts carbon dioxide gas to organic 
carbon, and respiration cycles the organic carbon back into 
carbon dioxide gas. Long-term storage of organic carbon 
occurs when matter from living organisms is buried deep 
underground and becomes fossilized. Volcanic activity and, 
more recently, human emissions, bring this stored carbon back 
into the carbon cycle. (credit: modification of work by John M. 
Evans and Howard Perlman, USGS) 


The Biological Carbon Cycle 


Living organisms are connected in many ways, even between ecosystems. 
A good example of this connection is the exchange of carbon between 
autotrophs and heterotrophs within and between ecosystems by way of 
atmospheric carbon dioxide. Carbon dioxide is the basic building block that 


most autotrophs use to build multi-carbon, high energy compounds, such as 
glucose. The energy harnessed from the sun is used by these organisms to 
form the covalent bonds that link carbon atoms together. These chemical 
bonds thereby store this energy for later use in the process of respiration. 
Most terrestrial autotrophs obtain their carbon dioxide directly from the 
atmosphere, while marine autotrophs acquire it in the dissolved form 
(carbonic acid, HyCO3 _). However carbon dioxide is acquired, a by-product 
of the process is oxygen. Photosynthetic organisms are responsible for the 
approximately 21 percent oxygen content of the atmosphere that we 
observe today. 


Heterotrophs and autotrophs are partners in biological carbon exchange 
(especially the primary consumers, largely herbivores). Heterotrophs 
acquire the high-energy carbon compounds from the autotrophs by 
consuming them, and breaking them down by respiration to obtain cellular 
energy, such as ATP. The most efficient type of respiration, aerobic 
respiration, requires oxygen obtained from the atmosphere or dissolved in 
water. Thus, there is a constant exchange of oxygen and carbon dioxide 
between the autotrophs (which need the carbon) and the heterotrophs 
(which need the oxygen). Gas exchange through the atmosphere and water 
is one way that the carbon cycle connects all living organisms on Earth. 


The Biogeochemical Carbon Cycle 


The movement of carbon through the land, water, and air is complex, and in 
many cases, it occurs much more slowly geologically than it does between 
living organisms. Carbon is stored for long periods in what are known as 
carbon reservoirs, which include the atmosphere, bodies of liquid water 
(mostly oceans), ocean sediment, soil, land sediments (including fossil 
fuels), and the Earth’s interior. 


As stated, the atmosphere is a major reservoir of carbon in the form of 
carbon dioxide and is essential to the process of photosynthesis. The level 
of carbon dioxide in the atmosphere is greatly influenced by the reservoir of 
carbon in the oceans. The exchange of carbon between the atmosphere and 
water reservoirs influences how much carbon is found in each location, and 


each one affects the other reciprocally. Carbon dioxide (CO>) from the 
atmosphere dissolves in water and combines with water molecules to form 
carbonic acid, and then it ionizes to carbonate and bicarbonate ions ([link]) 


Step 2: CO2 (dissolved) + HzO = H2CO3 (carbonic acid) 


Step 4: HCO3- = H* + CO3* (carbonate ion) 


Carbon dioxide reacts with water 
to form bicarbonate and carbonate 
ions. 


The equilibrium coefficients are such that more than 90 percent of the 
carbon in the ocean is found as bicarbonate ions. Some of these ions 
combine with seawater calcium to form calcium carbonate (CaCO3), a 
major component of marine organism shells. These organisms eventually 
form sediments on the ocean floor. Over geologic time, the calcium 
carbonate forms limestone, which comprises the largest carbon reservoir on 
Earth. 


On land, carbon is stored in soil as a result of the decomposition of living 
organisms (by decomposers) or from weathering of terrestrial rock and 
minerals. This carbon can be leached into the water reservoirs by surface 
runoff. Deeper underground, on land and at sea, are fossil fuels: the 
anaerobically decomposed remains of plants that take millions of years to 
form. Fossil fuels are considered a non-renewable resource because their 
use far exceeds their rate of formation. A non-renewable resource, such as 
fossil fuel, is either regenerated very slowly or not at all. Another way for 
carbon to enter the atmosphere is from land (including land beneath the 
surface of the ocean) by the eruption of volcanoes and other geothermal 
systems. Carbon sediments from the ocean floor are taken deep within the 
Earth by the process of subduction: the movement of one tectonic plate 


beneath another. Carbon is released as carbon dioxide when a volcano 
erupts or from volcanic hydrothermal vents. 


Carbon dioxide is also added to the atmosphere by the animal husbandry 
practices of humans. The large numbers of land animals raised to feed the 
Earth’s growing population results in increased carbon dioxide levels in the 
atmosphere due to farming practices and the respiration and methane 
production. This is another example of how human activity indirectly 
affects biogeochemical cycles in a significant way. Although much of the 
debate about the future effects of increasing atmospheric carbon on climate 
change focuses on fossils fuels, scientists take natural processes, such as 
volcanoes and respiration, into account as they model and predict the future 
impact of this increase. 


The Nitrogen Cycle 


Nitrogen is an essential nutrient for living processes; it is a major 
component of proteins and nucleic acids. Proteins are important biological 
molecules because all cellular activities are driven by proteins. Nucleic 
Acids are the building blocks of DNA (hereditary material). Nitrogen is 
often the limiting nutrient (necessary for growth) on terrestrial ecosystems 
[link]. 


Getting nitrogen into the living world is difficult. Plants and phytoplankton 
are not equipped to incorporate nitrogen from the atmosphere (which exists 
as tightly bonded, triple covalent Nz) even though this molecule comprises 
approximately 78 percent of the atmosphere. Nitrogen enters the living 
world via free-living and symbiotic bacteria, which incorporate nitrogen 
into their macromolecules through nitrogen fixation (conversion of N>). 
Cyanobacteria live in most aquatic ecosystems where sunlight is present; 
they play a key role in nitrogen fixation. Cyanobacteria are able to use 
inorganic sources of nitrogen to “fix” nitrogen. Rhizobium bacteria live 
symbiotically in the root nodules of legumes (such as peas, beans, and 
peanuts) and provide them with the organic nitrogen they need. Free-living 
bacteria, such as Azotobacter, are also important nitrogen fixers. In 
addition, humans industrially fix nitrogen to produce artificial fertilizers. 


Organic nitrogen is especially important to the study of ecosystem 
dynamics since many ecosystem processes, such as primary production and 
decomposition, are limited by the available supply of nitrogen. As shown in 
[link], the nitrogen that enters living systems by nitrogen fixation is 
successively converted from organic nitrogen back into nitrogen gas by 
bacteria. This process occurs in three steps in terrestrial systems: 
ammonification, nitrification, and denitrification. First, the ammonification 
process converts nitrogenous waste from living animals or from the remains 
of dead animals into ammonium (NH,’) by certain bacteria and fungi. 
Second, the ammonium is converted to nitrites (NO, _) by nitrifying 
bacteria, such as Nitrosomonas, through nitrification. Subsequently, nitrites 
are converted to nitrates (NO3_) by similar organisms. Third, the process of 
denitrification occurs, whereby bacteria, such as Pseudomonas and 
Clostridium, convert the nitrates into nitrogen gas, allowing it to re-enter 
the atmosphere. 


suire Nitrogen Cycle 


Denitrification 
by bacteria 


| 
Nitrification by Nitrogenous 
bacteria to NO; wastes in soil 


nN 
y \ \ 4 
| v 
Ammonification Nitrogen 


Nitrification by by bacteria and <__ fixation 
bacteria to NOz »“Y fungi to NH,* > ' by bacteria 


Nitrogen enters the living world from the atmosphere via 
nitrogen-fixing bacteria. This nitrogen and nitrogenous waste 


from animals is then processed back into gaseous nitrogen by 

soil bacteria, which also supply terrestrial food webs with the 

organic nitrogen they need. (credit: modification of work by 
John M. Evans and Howard Perlman, USGS) 


Human activity can release nitrogen into the environment by two primary 
means: the combustion of fossil fuels, which releases different nitrogen 
oxides, and by the use of artificial fertilizers in agriculture, which are then 
washed into lakes, streams, and rivers by surface runoff. Atmospheric 
nitrogen is associated with several effects on Earth’s ecosystems including 
the production of acid rain (as nitric acid, HNO3) and greenhouse gas (as 
nitrous oxide, N»O) potentially causing climate change. A major effect from 
fertilizer runoff is saltwater and freshwater eutrophication, a process 
whereby nutrient runoff causes the excess growth of microorganisms, 
depleting dissolved oxygen levels and killing ecosystem fauna. 


A similar process occurs in the marine nitrogen cycle, where the 
ammonification, nitrification, and denitrification processes are performed 
by marine bacteria. Some of this nitrogen falls to the ocean floor as 
sediment, which can then be moved to land in geologic time by uplift of the 
Earth’s surface and thereby incorporated into terrestrial rock. Although the 
movement of nitrogen from rock directly into living systems has been 
traditionally seen as insignificant compared with nitrogen fixed from the 
atmosphere, a recent study showed that this process may indeed be 
significant and should be included in any study of the global nitrogen cycle. 
[footnote] 

Scott L. Morford, Benjamin Z. Houlton, and Randy A. Dahlgren, 
“Increased Forest Ecosystem Carbon and Nitrogen Storage from Nitrogen 
Rich Bedrock,” Nature 477, no. 7362 (2011): 78-81. 


The Phosphorus Cycle 


Phosphorus is another essential nutrient for living processes; it is a major 
component of nucleic acids, phospholipids, and, as calcium phosphate, 


makes up the supportive components of our bones. Phosphorus is often the 
limiting nutrient (necessary for growth) in aquatic ecosystems ([link]). 


Phosphorus occurs in nature as the phosphate ion (PO,° ). In addition to 
phosphate runoff as a result of human activity (mined and used to make a 
artificial fertilizer), natural surface runoff occurs when it is leached from 
phosphate-containing rock by weathering, thus sending phosphates into 
rivers, lakes, and the ocean. This rock has its origins in the ocean. 
Phosphate-containing ocean sediments form primarily from the bodies of 
ocean organisms and from their excretions. However, in remote regions, 
volcanic ash, aerosols, and mineral dust may also be significant phosphate 
sources. This sediment then is moved to land over geologic time by the 
uplifting of areas of the Earth’s surface. Phosphorus is . 


Phosphorus is also reciprocally exchanged between phosphate dissolved in 
the ocean and marine ecosystems. The movement of phosphate from the 
ocean to the land and through the soil is extremely slow, with the average 
phosphate ion having an oceanic residence time between 20,000 and 
100,000 years. 


In nature, phosphorus exists as the phosphate ion (PO,° ). 
Weathering of rocks and volcanic activity releases phosphate 
into the soil, water, and air, where it becomes available to 
terrestrial food webs. Phosphate enters the oceans via surface 
runoff, groundwater flow, and river flow. Phosphate dissolved 
in ocean water cycles into marine food webs. Some phosphate 
from the marine food webs falls to the ocean floor, where it 
forms sediment. (credit: modification of work by John M. 
Evans and Howard Perlman, USGS) 


Excess phosphorus and nitrogen entering these ecosystems from fertilizer 
runoff, and from sewage, causes excessive growth of microorganisms. This 
is known as eutrophication (the enrichment of bodies of fresh water by 
inorganic plant nutrients). These abundant microorganism "blooms" then 
die and decay, which can increase the rate of sedimentation. But the most 
important biological effect is to deplete the oxygen which is dissolved in the 
water. Oxygen is critical for most aquatic organisms, and oxygen depletion 


leads to the death of many of the larger organisms, such as shellfish and 
finfish. This process is responsible for dead zones in lakes and at the 
mouths of many major rivers ([link]). 


Particulate Organic Carbon (mg/m') Population Density (persons/km’) Dead Zone Size (km’) 
wn © 


unkown « . 
10 20 50 100 200 $00 1,000 ' 10 100 1,000 10k 100k 0.1 § 10 100 Ik 10k 


Dead zones occur when phosphorus and nitrogen from 
fertilizers cause excessive growth of microorganisms, which 
depletes oxygen and kills fauna. Worldwide, large dead zones 
are found in coastal areas of high population density. (credit: 
NASA Earth Observatory) 


A dead zone is an area within a freshwater or marine ecosystem where 
large areas are depleted of their normal flora and fauna; these zones can be 
caused by eutrophication, oil spills, dumping of toxic chemicals, and other 
human activities. The number of dead zones has been increasing for several 
years, and more than 400 of these zones were present as of 2008. One of the 
worst dead zones is off the coast of the United States in the Gulf of Mexico, 
where fertilizer runoff from the Mississippi River basin has created a dead 
zone of over 8463 square miles. Phosphate and nitrate runoff from 


fertilizers also negatively affect several lake and bay ecosystems including 
the Chesapeake Bay in the eastern United States. 


Biogeography 


Introduction 

"Biology is a science of three dimensions. The first is the study of each 
species across all levels of biological organization, molecule to cell to 
organism to population to ecosystem. The second dimension is the diversity 
of all species in the biosphere. The third dimension is the history of each 
species in turn, comprising both its genetic evolution and the environmental 
change that drove the evolution. Biology, by growing in all three 
dimensions, is progressing toward unification and will continue to do so." - 
Edward O. Wilson, in 'Systematics and the Future of Biology', Systematics 
and the Origin of Species: on Ernst Mayr's 100th anniversary, Volume 102, 
Issues 22-26 (2005) 


Many forces influence the communities of living organisms present in 
different parts of the biosphere (all of the parts of Earth inhabited by life). 
The biosphere extends into the atmosphere (several kilometers above Earth) 
and into the depths of the oceans. Despite its apparent vastness to an 
individual human, the biosphere occupies only a minute space when 
compared to the known universe. Many abiotic forces influence where life 
can exist and the types of organisms found in different parts of the 
biosphere. The abiotic factors influence the distribution of biomes: large 
areas of land with similar climate, flora, and fauna. 


Biogeography 


Biogeography is the study of the geographic distribution of living things 
and the abiotic factors that affect their distribution. Abiotic factors such as 
temperature and rainfall vary based mainly on latitude and elevation. As 
these abiotic factors change, the composition of plant and animal 
communities also changes. For example, if you were to begin a journey at 
the equator and walk north, you would notice gradual changes in plant 
communities. At the beginning of your journey, you would see tropical wet 
forests with broad-leaved evergreen trees, which are characteristic of plant 
communities found near the equator. As you continued to travel north, you 
would see these broad-leaved evergreen plants eventually give rise to 
seasonally dry forests with scattered trees. You would also begin to notice 


changes in temperature and moisture. At about 30 degrees north, these 
forests would give way to deserts, which are characterized by low 
precipitation. 


Moving farther north, you would see that deserts are replaced by grasslands 
or prairies. Eventually, grasslands are replaced by deciduous temperate 
forests. These deciduous forests give way to the boreal forests found in the 
subarctic, the area south of the Arctic Circle. Finally, you would reach the 
Arctic tundra, which is found at the most northern latitudes. This trek north 
reveals gradual changes in both climate and the types of organisms that 
have adapted to environmental factors associated with ecosystems found at 
different latitudes. However, different ecosystems exist at the same latitude 
due in part to abiotic factors such as atmospheric jet streams, and other 
ocean currents. A simplified model of the air circulation at different 
latitudes, which is a primary cause of the climate and ecozones at different 
latitudes, is shown in the figure below. There are six rotating cells of air in 
the upper atmosphere (three north of the equator, and three south of the 
equator) that, combined with the earth's rotation, create the earth's climate 
and influence the distribution of plants and animals. 

Global Air Circulation patterns 


Tropopause 

in arctic zone 

Tropopause 
in temperate 


Polar cell 


Mid-latitude cell 


Hadley cell 


Intertropical 
convergence 
zone 


0° 


Hadley cell 


30°S 


Mid-latitude cell 


Polar cell 


Simplified diagram of the upper air circulation patterns that help create 
the earth's climate. (modified from Wikimedia Commons). Rising and 
descending air creates three "cells" that encircle the globe. High 
pressure areas are created in regions where the air descends; low 
pressure areas arise where the air is ascending. Descending air has lost 
much of its moisture (there are lots of thunderstorms in the tropics!), 
and so moisture is absorbed in those regions where dryer air returns to 
the surface (e.g. 30 degrees N and 30 degrees S). This results in a band 
of desert regions at those latitudes. 


Ecologists who study biogeography are especially interested in patterns of 
species distribution. No species exists everywhere; most are found in 
relatively small areas of the world. For example, the Venus flytrap is 
endemic to a small area in North and South Carolina. An endemic species 
is one which is naturally found only in a specific geographic area that is 
usually restricted in size. Other species are generalists: species which live in 
a wide variety of geographic areas; the raccoon, for example, is native to 
most of North and Central America. Some birds (e.g. Osprey, Pandion 
halietus) are found in appropriate habitats on several continents. 


Species distribution patterns are based on biotic and abiotic factors, and are 
also influenced by events occurring during the very long periods of time 
required for species evolution. Early studies of biogeography were closely 
linked to the emergence of evolutionary thinking in the eighteenth century, 
and, in fact, observations of these patterns helped Wallace and Darwin 
formulate the theory of evolution. Some of the most distinctive assemblages 
of plants and animals occur in regions that have been physically separated 
for millions of years by geographic barriers. Biologists estimate that 
Australia, for example, has between 600,000 and 700,000 species of plants 
and animals; 92% of the plant species, and 83% of the mammal species in 
Australia are endemic (found on no other continent). See the Figure below 
for a couple of examples. This is a consequence of the fact that Australia 
and Asia have been geographically separated for at least 50 million years. 


Australia is home to many endemic species. The (a) 
wallaby (Wallabia bicolor), a medium-sized member 
of the kangaroo family, is a pouched mammal, or 
marsupial. The (b) echidna (Tachyglossus aculeatus) 
is an egg-laying mammal. (credit a: modification of 
work by Derrick Coetzee; credit b: modification of 
work by Allan Whittome) 


Sometimes ecologists discover unique patterns of species distribution by 
determining where species are not found. Hawaii, for example, has no 
native land species of reptiles or amphibians, and has only one native 
terrestrial mammal, the hoary bat. Most of New Guinea lacks placental 
mammals, and prior to human settlement, there were no land mammals in 
New Zealand except for three species of bats. 


Plants can be endemic or generalists: endemic plants are found only on 
specific regions of the Earth, while generalists are found on many regions. 
Isolated land masses—such as Australia, Hawaii, and Madagascar—often 
have large numbers of endemic plant species. Some of these plants are 
endangered due to human activity. The forest gardenia (Gardenia 
brighamii), for instance, is endemic to Hawaii; only an estimated 15—20 
trees are thought to exist ({link]). 


Listed as federally 
endangered, the forest 
gardenia is a small tree 

with distinctive flowers. It 
is found only in five of the 
Hawaiian Islands in small 


populations consisting of a 
few individual specimens. 
(credit: Forest & Kim 
Starr) 


Energy Sources 


The distribution of organisms is also influenced by the availability of 
energy in their environment. Energy from the sun is captured by green 
plants, algae, cyanobacteria, and photosynthetic protists. These organisms 
convert solar energy into the chemical energy needed by all living things. 
Light availability can be an important force directly affecting the evolution 
of adaptations in photosynthesizers. For instance, plants in the understory of 
a temperate forest are shaded when the trees above them in the canopy 
completely leaf out in the late spring. Not surprisingly, understory plants 
have adaptations to successfully capture available light. One such 


adaptation is the rapid growth of spring ephemeral plants such as the spring 
beauty ((link]). These spring flowers achieve much of their growth and 
finish their life cycle (reproduce) early in the season before the trees in the 
canopy develop leaves. 


The spring beauty is an 
ephemeral spring plant 
that flowers early in the 
spring to avoid competing 
with larger forest trees for 
sunlight. (credit: John 
Beetham) 


In aquatic ecosystems, the availability of light may be limited because 
sunlight is absorbed by water, plants, suspended particles, and resident 
microorganisms. Toward the bottom of a lake, pond, or ocean, there may be 
a zone that light cannot reach. Photosynthesis cannot take place there and, 
as aresult, a number of adaptations have evolved that enable living things 
to survive in these situations. For instance, aquatic plants have 
photosynthetic tissue near the surface of the water; the broad, floating 
leaves of a water lily ensure that this organism gets the light it needs to 


survive. In totally dark environments such as hydrothermal vents in the 
deep ocean, some bacteria extract energy from inorganic chemicals using 
chemosynthesis, a metabolic pathway similar to photosynthesis. You'll learn 
more about those pathways in a later module. 


The availability of inorganic nutrients in aquatic systems is also an 
important aspect of energy or photosynthesis. Many organisms sink to the 
bottom of the ocean when they die in the open water; when this occurs, the 
nutrients and energy in that organism are out of circulation for some time, 
unless ocean upwelling occurs. Ocean upwelling is the rising of deep 
ocean waters that occurs when prevailing winds blow along surface waters 
near a coastline ([link]). As the wind pushes ocean waters offshore, water 
from the bottom of the ocean moves up to replace this water. As a result, the 
nutrients once contained in dead organisms become available for reuse by 
other living organisms. 


Coastline 


Ocean upwelling is an important 
process that recycles nutrients 
and energy in the ocean. As 
wind (green arrows) pushes 
offshore, it causes water from 
the ocean bottom (red arrows) to 


move to the surface, bringing up 
nutrients from the ocean depths. 


In freshwater systems, the recycling of nutrients occurs in response to air 
temperature changes. The nutrients at the bottom of lakes are recycled twice 
each year: in the spring and fall turnover. The spring and fall turnover is a 
seasonal process that recycles nutrients and oxygen from the bottom of a 
freshwater ecosystem to the top ({link]). These turnovers are caused by the 
formation of a thermocline: a layer of water with a temperature that is 
significantly different from that of the surrounding layers. In wintertime, the 
surface of lakes found in many northern regions is frozen. However, the 
water under the ice is slightly warmer, and the water at the bottom of the 
lake is warmer yet at 4 °C to 5 °C (39.2 °F to 41 °F). Water is densest at 4 
°C; therefore, the deepest water is also the densest. The deepest water is 
oxygen poor because the decomposition of organic material at the bottom of 
the lake uses up available oxygen that cannot be replaced in the winter. 
There is little or no photosynthesis in that season, and any diffusion of 
oxygen from the atmosphere is blocked by the surface ice layer. 


Note: 
Seasonal turnovers in lakes 


o° 4° 
79 a 
ao 4° 
4° 4° 


Winter Spring turnover 


10° 
g° 
70 
40 


Summer stratification Fall turnover 


21° 


The spring and fall turnovers are important 
processes in freshwater lakes that act to move the 
nutrients and oxygen at the bottom of deep lakes to 
the top. Turnover occurs because water has a 
maximum density at 4 °C. Surface water 
temperature changes as the seasons progress, and 
denser water sinks. 


In springtime, air temperatures increase and surface ice melts. When the 
temperature of the surface water begins to reach 4 °C, the water becomes 
heavier and sinks to the bottom. The water at the bottom of the lake is then 
displaced by the heavier surface water and, thus, rises to the top. As that 
water rises to the top, the sediments and nutrients from the lake bottom are 
brought along with it. During the summer months, the lake water stratifies, 
or forms layers, with the warmest water at the lake surface. 


As air temperatures drop in the fall, the temperature of the lake water cools 
to 4 °C; therefore, this causes fall turnover as the heavy cold water sinks 
and displaces the water at the bottom. The oxygen-rich water at the surface 
of the lake then moves to the bottom of the lake, while the nutrients at the 
bottom of the lake rise to the surface ([link]). During the winter, the oxygen 
at the bottom of the lake is used by decomposers and other organisms 
requiring oxygen, such as fish. 


Temperature 


In addition to its effects on the density of water, temperature affects the 
physiology (and the biogeographic distribution) of living things. 
Temperature exerts an important influence on living things because few 
organisms can survive at temperatures below 0° C (32° F), due to metabolic 
constraints. It is also rare for living things to survive at temperatures 


exceeding 45° C (113° F). This is primarily due to temperature effects on 
the proteins known as enzymes. Enzymes are typically most efficient within 
a narrow and specific range of temperatures; enzyme denaturation (damage) 
can occur at higher temperatures, and enzymes do not work fast enough at 
lower temperatures. Therefore, organisms either must maintain an internal 
temperature that keeps their enzymes functioning, or they must inhabit an 
environment that will keep the body within a temperature range that 
supports metabolism. Some animals have adapted to enable their bodies to 
survive significant temperature fluctuations. Some Antarctic fish live at 
temperatures below freezing, and hibernating Arctic ground squirrels 
(Urocitellus parryii) can survive if their body temperature drops below 
freezing. Similarly, some bacteria are adapted to surviving in extremely hot 
environments, such as geysers, boiling mud pits or deep-ocean 
hydrothermal vents. Such bacteria are examples of extremophiles: 
organisms that thrive in extreme environments. 


Temperature can also limit the distribution of living things. Animals in 
regions with large temperature fluctuations may respond with various 
adaptations, such as migration, in order to survive. Migration, the 
movement from one place to another, is an adaptation found in many 
animals, including many that inhabit seasonally cold climates. Migration 
solves problems related to temperature, locating food, and finding a mate. 
In migration, for instance, the Arctic Tern (Sterna paradisaea) makes a 
40,000 km (24,000 mi) round trip flight each year between its feeding 
grounds in the southern hemisphere and its breeding grounds in the Arctic. 
Monarch butterflies (Danaus plexippus) live in the eastern United States in 
the warmer months and migrate to Mexico and the southern United States 
in the wintertime. Some species of mammals also make migratory forays. 
Reindeer (Rangifer tarandus) travel about 5,000 km (3,100 mi) each year to 
find food. Amphibians and reptiles are more limited in their distribution 
because they lack migratory ability. Not all animals that can migrate do so: 
migration carries risk and comes at a high energy cost. 


Other successful adaptations allow animals to stay in place and not migrate. 
Some animals hibernate or estivate to survive hostile temperatures. 
Hibernation enables animals to survive cold conditions, and estivation 
allows animals to survive the hostile conditions of a hot, dry climate. 


Animals that hibernate or estivate enter a state known as torpor: a condition 
in which their metabolic rate is significantly lowered. This enables the 
animal to wait until its environment better supports its survival. Some 
amphibians, such as the wood frog (Rana sylvatica), have an antifreeze-like 
chemical in their cells, which prevents water in the cell from freezing and 
expanding until the cell is destroyed. 


Water 


Water is required by all living things because it is critical for cellular 
processes. Since terrestrial organisms lose water to the environment by 
simple diffusion, they have evolved many adaptations to retain water. 


e Plants have a number of interesting features on their leaves, such as 
leaf hairs and a waxy cuticle, that serve to decrease the rate of water 
loss via transpiration. 

e Animals that live in very dry environments have many adaptations that 
allow them to survive without water intake. Kangaroo rats, which live 
in arid areas in the US and Mexico, obtain most of their water from 
metabolism of the carbohydrates and lipids in the seeds that make up 
their diet. They almost never drink water, and would rarely see liquid 
water in their normal habitats. They also produce very small amounts 
of highly concentrated, nearly crystalline, urine. 

e Freshwater organisms are surrounded by water and are constantly in 
danger of having water rush into their cells because of osmosis. Many 
adaptations of organisms living in freshwater environments have 
evolved to ensure that solute concentrations in their bodies remain 
within appropriate levels. One such adaptation is the excretion of 
dilute urine. 

e Marine organisms are surrounded by water with a higher solute 
concentration than the organism and, thus, are in danger of losing 
water to the environment because of osmosis. These organisms have 
morphological and physiological adaptations to retain water and 
release solutes into the environment. For example, Marine Iguanas 
(Amblyrhynchus cristatus), sneeze out water vapor that is high in salt 


in order to maintain solute concentrations within an acceptable range 
while swimming in the ocean and eating marine plants. 


Inorganic Nutrients and Soil 


Inorganic nutrients, such as nitrogen and phosphorus, are important in the 
distribution and the abundance of living things. Plants obtain these 
inorganic nutrients from the soil when water moves into the plant through 
the roots. Therefore, soil structure (particle size of soil components), soil 
pH, and soil nutrient content play an important role in the distribution of 
plants. Animals obtain inorganic nutrients from the food they consume. 
Therefore, animal distributions are related to the distribution of what they 
eat. In some cases, animals will follow their food resource as it moves 
through the environment. 


Other Aquatic Factors 


Some abiotic factors, such as oxygen, are important in aquatic ecosystems 
as well as terrestrial environments. Terrestrial animals obtain oxygen from 
the air they breathe. Oxygen availability can be an issue for organisms 
living at very high elevations, however, where there are fewer molecules of 
oxygen in the air. In aquatic systems, the concentration of dissolved oxygen 
is related to water temperature and the speed at which the water moves. 
Cold water has more dissolved oxygen than warmer water. In addition, 
salinity, current, and tide can be important abiotic factors in aquatic 
ecosystems. 


Other Terrestrial Factors 


Wind can be an important abiotic factor because it influences the rate of 
evaporation and transpiration. The physical force of wind is also important 
because it can move soil, water, or other abiotic factors, as well as an 
ecosystem’s organisms. 


Fire is another terrestrial factor that can be an important agent of 
disturbance in terrestrial ecosystems. Some organisms are adapted to fire 
and, thus, require the high heat associated with fire to complete a part of 
their life cycle. For example, the jack pine—a coniferous tree—requires 
heat from fire for its seed cones to open ((link]). Through the burning of 
pine needles, fire adds nitrogen to the soil and limits competition by 
destroying undergrowth. Closer to home, the tallgrass prairie ecosystem of 
the Kansas Flint Hills is dependent on fire and grazing by large herbivores 
(formerly bison, now cattle). In the absence of such disturbances, the 
grasslands of the Flint Hills become scrubby cedar forests in just a few 
decades. 


(b) 


(a) The mature cones of the jack pine (Pinus banksiana) open only 
when exposed to high temperatures, such as during a forest fire. A 
fire is likely to kill most vegetation, so a seedling that germinates 
after a fire is more likely to receive ample sunlight than one that 
germinates under normal conditions. (credit: USDA) (b) A controlled 
burn moves across the Konza Prairie Biological Station. Fire is a 
critical determinant in the maintenance of the tallgrass prairie 
ecosystem. (photo by D.A. Rintoul) 


Abiotic Factors Influencing Plant Growth 


Temperature and moisture are important influences on plant production and 
the amount of organic matter available to other organisms (net primary 
productivity). Net primary productivity is an estimation of all of the 
organic matter available to organisms in other trophic levels; it is calculated 
as the total amount of carbon incorporated into plant tissues per year minus 
the amount that is used during plant metabolism. In terrestrial 
environments, net primary productivity is estimated by measuring the 
aboveground biomass per unit area, which is the total mass of living plants, 
excluding roots. This means that a large percentage of plant biomass which 
exists underground is not included in this measurement. Net primary 
productivity is an important variable when considering differences between 
biomes. Very productive biomes have a high level of net primary 
productivity, i.e., a large amount of energy at the primary producer trophic 
level. 


Annual biomass production is directly related to the abiotic components of 
the environment. Environments with the greatest amount of biomass have 
conditions in which photosynthesis, plant growth, and the resulting net 
primary productivity are optimized. The climate of these areas is warm, 
wet, and usually stable year-round. Photosynthesis can proceed at a high 
rate, enzymes can work most efficiently, and stomata can remain open 
without the risk of excessive transpiration. Together, these factors lead to 
the maximal amount of carbon dioxide (CO>) moving into the plant, 
resulting in high biomass production. This biomass produces several 
important resources for other living things, including habitat and food. 
Conversely, dry and cold environments have lower photosynthetic rates and 
therefore less biomass. The animal communities, and the complexity of the 
food webs, will also be affected by the decrease in available energy at the 
primary producer level. 


Biomes 


"The sea, the woods, the mountains, all suffer in comparison with the 
prairie...The prairie has a stronger hold upon the senses. Its sublimity arises 
from its unbounded extent, its barren monotony and desolation, its still, 
unmoved, calm, stern, almost self-confident grandeur, its strange power of 
deception, its want of echo, and, in fine, its power of throwing a man back 
upon himself." - Albert Pike (1831-32, Journeys in the Prairie) 

Konza Prairie 


A grassland Biome - Konza Prairie, near Manhattan, KS. 
(photograph by David A. Rintoul) 


The prairie grassland biome, described by Pike, is one of the Earth's great 
biomes. But what is a biome, exactly? Biomes are large areas of land (or 
water) with similar climate, flora, and fauna. The Earth’s biomes are 
categorized into two major groups: terrestrial and aquatic. Terrestrial 
biomes are based on land, while aquatic biomes include both ocean and 
freshwater biomes. The eight major terrestrial biomes on Earth are each 
distinguished by characteristic temperatures and amount of precipitation. 
Comparing the annual totals of precipitation and fluctuations in 


precipitation from one biome to another provides clues as to the importance 
of abiotic factors in the distribution of biomes. Temperature variation on a 
daily and seasonal basis is also important for predicting the geographic 
distribution of the biome and the vegetation type in the biome. The 
distribution of these biomes shows that the same biome can occur in 
geographically distinct areas with similar climates ([link]). 


Note: 
Biomes 


Mi Tropical forest Savanna MS Desert @ Chaparral {™ Temperate forest 
{Boreal forest @ Tundra @® Mountains ) Polar ice (Temperate grassland 


Each of the world’s major biomes is distinguished by 
characteristic temperatures and amounts of precipitation. 
Polar ice and mountains are also shown. 


Rainforest 


Rainforests are also referred to as tropical rainforests. This biome is found 
in equatorial regions (({link]). The vegetation is characterized by plants with 
broad leaves that fall off throughout the year. Unlike the trees of deciduous 
forests, the trees in this biome do not have a seasonal loss of leaves 


associated with variations in temperature and sunlight; these forests are 
“evergreen” year-round. 


The temperature and sunlight profiles of tropical rainforests are very stable 
in comparison to that of other terrestrial biomes, with the temperatures 
ranging from 20 °C to 34 °C (68 °F to 93 °F). When one compares the 
annual temperature variation of tropical rainforests with that of other forest 
biomes, the lack of seasonal temperature variation in the tropical rainforest 
becomes apparent. This lack of seasonality leads to year-round plant 
growth, rather than the seasonal (spring, summer, and fall) growth seen in 
other biomes. In contrast to other ecosystems, tropical ecosystems do not 
have long days and short days during the yearly cycle. Instead, a constant 
daily amount of sunlight (11-12 hrs per day) provides more solar radiation, 
thereby, a longer period of time for plant growth. 


The annual rainfall in tropical rainforests ranges from 125 to 660 cm (50— 
200 in) with some monthly variation. While sunlight and temperature 
remain fairly consistent, annual rainfall is highly variable. Tropical 
rainforests have wet months in which there can be more than 30 cm (11-12 
in) of precipitation, as well as dry months in which there are fewer than 10 
cm (3.5 in) of rainfall. However, the driest month of a tropical rainforest 
still exceeds the annual rainfall of some other biomes, such as deserts. 


Tropical rainforests have high net primary productivity because the annual 
temperatures and precipitation values in these areas are ideal for plant 
growth. Therefore, the extensive biomass present in the tropical rainforest 
leads to plant communities with very high species diversities ({link]). 
Tropical rainforests have more species of trees than any other biome; on 
average between 100 and 300 species of trees are present in a single hectare 
(2.5 acres) of the Amazon region of South America. One way to visualize 
this is to compare the distinctive horizontal layers within the tropical 
rainforest biome. On the forest floor is a sparse layer of plants and decaying 
plant matter. Above that is an understory of short shrubby foliage. A layer 
of trees rises above this understory and is topped by a closed upper canopy 
—the uppermost overhead layer of branches and leaves. Some additional 
trees emerge through this closed upper canopy. These layers provide diverse 
and complex habitats for the variety of plants, fungi, animals, and other 


organisms within the tropical rainforests. For instance, epiphytes are plants 
that grow on other plants, which typically are not harmed. Epiphytes are 
found throughout tropical rainforest biomes. Many species of animals use 
the variety of plants and the complex structure of the tropical rainforests for 
food and shelter. Some organisms live several meters above ground and 
have adapted to this arboreal lifestyle. 


Tropical rain forests, such as these 
forests of Madre de Dios, Peru, 
near the Amazon River, have high 
species diversity. (credit: 
Roosevelt Garcia) 


Savannas 


Savannas are grasslands with scattered trees, and they are located in Africa, 
South America, and northern Australia ({link]). Savannas are hot, tropical 
areas with temperatures averaging from 24 °C to 29 °C (75 °F to 84 °F) and 
an annual rainfall of 10—40 cm (3.9-15.7 in). Savannas have an extensive 
dry season; for this reason, forest trees do not grow as well as they do in the 
tropical wet forest (or other forest biomes). As a result, within the grasses 


and forbs (herbaceous flowering plants) that dominate the savanna, there 
are relatively few trees ((link]). Since fire is an important source of 
disturbance in this biome, plants have evolved well-developed root systems 
that allow them to quickly re-sprout after a fire. 


Savannas, like this one in Taita 
Hills Wildlife Sanctuary in Kenya, 
are dominated by grasses. (credit: 

Christopher T. Cooper) 


Deserts 


Deserts exist between 15 ° and 30 ° north and south latitude and are 
centered on the Tropics of Cancer and Capricorn ([link]). This biome is 
very dry; in some years, evaporation exceeds precipitation. Subtropical hot 
deserts can have daytime soil surface temperatures above 60 °C (140 °F) 
and nighttime temperatures approaching 0 °C (32 °F). In cold deserts, 
temperatures can be as high as 25 °C and can drop below -30 °C (-22 °F). 
Deserts are characterized by low annual precipitation of fewer than 30 cm 
(12 in) with little monthly variation and lack of predictability in rainfall. In 
some cases, the annual rainfall can be as low as 2 cm (0.8 in) in deserts 
located in central Australia (“the Outback”) and northern Africa. 


The vegetation and low animal diversity of this biome is closely related to 
this low and unpredictable precipitation. Very dry deserts lack perennial 
vegetation that lives from one year to the next; instead, many plants are 
annuals that grow quickly and reproduce when rainfall does occur, then 
they die. Many other plants in these areas are characterized by having a 
number of adaptations that conserve water, such as deep roots, reduced 
foliage, and water-storing stems (({link]). Seed plants in the desert produce 
seeds that can be in dormancy for extended periods between rains. 
Adaptations in desert animals include nocturnal behavior and burrowing. 


To reduce water loss, 
many desert plants have 
tiny leaves or no leaves at 
all. The leaves of ocotillo 
(Fouquieria splendens), 
shown here in the Sonora 
Desert near Gila Bend, 


Arizona, appear only after 
rainfall, and then are shed. 


Temperate Grasslands 


Temperate grasslands are found throughout central North America, where 
they are also known as prairies; they are also in Eurasia, where they are 
known as steppes ({link]). Temperate grasslands have pronounced annual 
fluctuations in temperature with hot summers and cold winters. The annual 
temperature variation produces specific growing seasons for plants. Plant 
growth is possible when temperatures are warm enough to sustain plant 
growth and when ample water is available, which occurs in the spring, 
summer, and fall. During much of the winter, temperatures are low, and 
water, which is stored in the form of ice, is not available for plant growth. 


Annual precipitation ranges from 25 cm to 75 cm (9.8—29.5 in). Because of 
relatively lower annual precipitation in temperate grasslands, there are few 
trees except for those found growing along rivers or streams. The dominant 
vegetation tends to consist of grasses and some prairies sustain populations 
of grazing animals [link]. The vegetation is very dense and the soils are 
fertile because the subsurface of the soil is packed with the roots and 
rhizomes (underground stems) of these grasses. The roots and rhizomes act 
to anchor plants into the ground and replenish the organic material (humus) 
in the soil when they die and decay. 


The American bison (Bison bison), more 
commonly called the buffalo, is a grazing 
mammal that once populated American 
prairies in huge numbers. (photograph by 
Eva Home) 


Fires, mainly caused by lightning, are a natural disturbance in temperate 
grasslands. When fire is suppressed in temperate grasslands, the vegetation 
eventually converts to scrub and dense forests. Often, the restoration or 
management of temperate grasslands requires the use of controlled burns to 
suppress the growth of trees and maintain the grasses. 


Deciduous Forest 


Deciduous forests are the most common biome in eastern North America, 
Western Europe, Eastern Asia, Chile, and New Zealand ((link]). This biome 
is found throughout mid-latitude regions. Temperatures range between -30 
°C and 30 °C (-22 °F to 86 °F) and drop to below freezing on an annual 
basis. These temperatures mean that temperate forests have defined 
growing seasons during the spring, summer, and early fall. Precipitation is 
relatively constant throughout the year and ranges between 75 cm and 150 
cm (29.5—59 in). 


Because of the moderate annual rainfall and temperatures, deciduous trees 
are the dominant plant in this biome ([link]). Deciduous trees lose their 
leaves each fall and remain leafless in the winter. Thus, no photosynthesis 
occurs in the deciduous trees during the dormant winter period. Each 
spring, new leaves appear as the temperature increases. Because of the 
dormant period, the net primary productivity of temperate forests is less 
than that of tropical wet forests. In addition, temperate forests show less 
diversity of tree species than tropical wet forest biomes. 


Deciduous trees are the dominant 
plant in the temperate forest. 
(credit: Oliver Herold) 


The trees of the deciduous forests leaf out and shade much of the ground; 
however, this biome is more open than tropical wet forests because trees in 
the temperate forests do not grow as tall as the trees in tropical wet forests. 
The soils of the deciduous forests are rich in inorganic and organic 
nutrients. This is due to the thick layer of leaf litter on forest floors. As this 
leaf litter decays, nutrients are returned to the soil. The leaf litter also 
protects soil from erosion, insulates the ground, and provides habitats for 
invertebrates (such as the pill bug or roly-poly, Armadillidium vulgare) and 
their predators, such as the red-backed salamander (Plethodon cinereus). 


Coniferous Forest 


The coniferous forest, also known as taiga or boreal forest, is found south of 
the Arctic Circle and across most of Canada, Alaska, Russia, and northern 
Europe ((link]). This biome has cold, dry winters and short, cool, wet 
summers. The annual precipitation is from 40 cm to 100 cm (15.7—39 in) 
and usually takes the form of snow. Little evaporation occurs because of the 
cold temperatures. 


The long and cold winters in the coniferous forest have led to the 
predominance of cold-tolerant cone-bearing plants. These are evergreen 
coniferous trees like pines, spruce, and fir, which retain their needle-shaped 
leaves year-round. Evergreen trees can photosynthesize earlier in the spring 
than deciduous trees because less energy from the sun is required to warm a 
needle-like leaf than a broad leaf. This benefits evergreen trees, which grow 
faster than deciduous trees in the coniferous forest. In addition, soils in 
coniferous forest regions tend to be acidic with little available nitrogen. 
Leaves are a nitrogen-rich structure and deciduous trees must produce a 
new set of these nitrogen-rich structures each year. Therefore, coniferous 
trees that retain nitrogen-rich needles may have a competitive advantage 
over the broad-leafed deciduous trees. 


The net primary productivity of coniferous forests is lower than that of 
deciduous forests and tropical rain forests. The above ground biomass of 
coniferous forests is high because these slow-growing tree species are long 
lived and accumulate standing biomass over time. Plant species diversity is 
less than that seen in deciduous forests and tropical rain forests. Coniferous 
forests lack the pronounced elements of the layered forest structure seen in 
tropical wet forests. The structure of a coniferous forest is often only a tree 
layer and a ground layer ({link]). When conifer needles are dropped, they 
decompose more slowly than broad leaves; therefore, fewer nutrients are 
returned to the soil to fuel plant growth. 


The coniferous forest (taiga) has 
low lying plants and conifer trees. 
(credit: L.B. Brubaker) 


Arctic Tundra 


The Arctic tundra lies north of the subarctic boreal forest and is located 
throughout the Arctic regions of the northern hemisphere ({link]). The 
average winter temperature is -34 °C (-34 °F) and the average summer 
temperature is from 3 °C to 12 °C (37 °F—52 °F). Plants in the arctic tundra 
have a very short growing season of approximately 10-12 weeks. However, 
during this time, there are almost 24 hours of daylight and plant growth is 
rapid. The annual precipitation of the Arctic tundra is very low with little 
annual variation in precipitation. And, as in the boreal forests, there is little 
evaporation due to the cold temperatures. 


Plants in the Arctic tundra are generally low to the ground ([link]). There is 
little species diversity, low net primary productivity, and low aboveground 
biomass. Deeper soils of the Arctic tundra may remain in a perennially 
frozen state referred to as permafrost. The permafrost makes it impossible 
for roots to penetrate deep into the soil and slows the decay of organic 
matter, which inhibits the release of nutrients from organic matter. During 
the growing season, the ground of the Arctic tundra can be completely 
covered with plants or lichens. 


if 


Low-growing plants such as 
shrub willow dominate the 
tundra landscape, shown here 
in the Arctic National Wildlife 
Refuge. (credit: USFWS Arctic 
National Wildlife Refuge) 


Aquatic Biomes 


Abiotic Factors Influencing Aquatic Biomes 


Introduction 

"There’s nothing wrong with enjoying looking at the surface of the ocean 
itself, except that when you finally see what goes on underwater, you 
realize that you’ve been missing the whole point of the ocean. Staying on 
the surface all the time is like going to the circus and staring at the outside 
of the tent." — Dave Barry 


Like terrestrial biomes, aquatic biomes are influenced by a series of abiotic 
factors. The aquatic medium—water— has different physical and chemical 
properties than air, however. Even if the water in a pond or other body of 
water is perfectly clear (there are no suspended particles), water, on its own, 
absorbs light. As one descends into a deep body of water, there will 
eventually be a depth which the sunlight cannot reach. While there are some 
abiotic and biotic factors in a terrestrial ecosystem that might obscure light 
(like fog, dust, or insect swarms), usually these are not permanent features 
of the environment. The importance of light in aquatic biomes is central to 
the communities of organisms found in both freshwater and marine 
ecosystems. In freshwater systems, stratification due to differences in 
density is perhaps the most critical abiotic factor and is related to the energy 
aspects of light. The thermal properties of water (rates of heating and 
cooling) are significant to the function of marine systems and have major 
impacts on global climate and weather patterns. Marine systems are also 
influenced by large-scale physical water movements, such as currents; these 
are less important in most freshwater lakes. 


The ocean is categorized by several areas or zones ([link]). All of the 
ocean’s open water is referred to as the pelagic realm. The benthic realm 
extends along the ocean bottom from the shoreline to the deepest parts of 
the ocean floor. Within the pelagic realm is the photic zone, which is the 
portion of the ocean that light can penetrate (approximately 200 m or 650 
ft). At depths greater than 200 m, light cannot penetrate; thus, this is 
referred to as the aphotic zone. The majority of the ocean is aphotic and 
lacks sufficient light for photosynthesis. The deepest part of the ocean, the 


Challenger Deep (in the Mariana Trench, located in the western Pacific 
Ocean), is about 11,000 m (about 6.8 mi) deep. To give some perspective on 
the depth of this trench, the ocean is, on average, 4267 m or 14,000 ft deep. 
These realms and zones are relevant to freshwater lakes as well. 


Note: 


Ocean Zones 


Neritic Intertidal 
zone zone 


; Oceanic zone 
1 


Pelagic realm 


The ocean is divided into different zones 
based on water depth and distance from the 
shoreline. 


Marine Biomes 


The ocean is the largest marine biome. It is a continuous body of salt water 
that is relatively uniform in chemical composition; it is a weak solution of 
mineral salts and decayed biological matter. Within the ocean, coral reefs 
are a second kind of marine biome. Estuaries, coastal areas where salt water 
and fresh water mix, form a third unique marine biome. 


Ocean 


The physical diversity of the ocean is a significant influence on plants, 
animals, and other organisms. The ocean is categorized into different zones 
based on how far light reaches into the water. Each zone has a distinct 
group of species adapted to the biotic and abiotic conditions particular to 
that zone. 


The intertidal zone, which is the zone between high and low tide, is the 
oceanic region that is closest to land ({link]). Generally, most people think 
of this portion of the ocean as a sandy beach. In some cases, the intertidal 
zone is indeed a sandy beach, but it can also be rocky or muddy. The 
intertidal zone is an extremely variable environment because of tides. 
Organisms are exposed to air and sunlight at low tide and are underwater 
during high tide. Therefore, living things that thrive in the intertidal zone 
are adapted to being dry for long periods of time. The shore of the intertidal 
zone is also repeatedly struck by waves, and the organisms found there are 
adapted to withstand damage from the pounding action of the waves 
({link]). The exoskeletons of shoreline crustaceans (such as the shore crab, 
Carcinus maenas) are tough and protect them from desiccation (drying out) 
and wave damage. Another consequence of the pounding waves is that few 
algae and plants establish themselves in the constantly moving rocks, sand, 
or mud. 


Sea urchins, mussel shells, and 
starfish are often found in the 


intertidal zone, shown here in 
Kachemak Bay, Alaska. (credit: 
NOAA) 


The neritic zone ([link]) extends from the intertidal zone to depths of about 
200 m (or 650 ft) at the edge of the continental shelf. Since light can 
penetrate this depth, photosynthesis can occur in the neritic zone. The water 
here contains silt and is well-oxygenated, low in pressure, and stable in 
temperature. Phytoplankton and floating Sargassum (a type of free-floating 
marine seaweed) provide a habitat for some sea life found in the neritic 
zone. Zooplankton, protists, small fishes, and shrimp are found in the neritic 
zone and are the base of the food chain for most of the world’s fisheries. 


Beyond the neritic zone is the open ocean area known as the oceanic zone 
({link]). Within the oceanic zone there is thermal stratification where warm 
and cold waters mix because of ocean currents. Abundant plankton serve as 
the base of the food chain for larger animals such as whales and dolphins. 
Nutrients are scarce and this is a relatively less productive part of the 
marine biome. When photosynthetic organisms and the protists and animals 
that feed on them die, their bodies fall to the bottom of the ocean where 
they remain; unlike freshwater lakes, the open ocean lacks a process for 
bringing the organic nutrients back up to the surface. The majority of 
organisms in the aphotic zone include sea cucumbers (phylum 
Echinodermata) and other organisms that survive on the nutrients contained 
in the dead bodies of organisms in the photic zone. 


Beneath the pelagic zone is the benthic realm, the deepwater region beyond 
the continental shelf ([link]). The bottom of the benthic realm is comprised 
of sand, silt, and dead organisms. Temperature decreases, remaining above 
freezing, as water depth increases. This is a nutrient-rich portion of the 
ocean because of the dead organisms that fall from the upper layers of the 
ocean. Because of this high level of nutrients, a diversity of fungi, sponges, 
sea anemones, marine worms, Sea stars, fishes, and bacteria exist. 


The deepest part of the ocean is the abyssal zone, which is at depths of 4000 
m or greater. The abyssal zone ([link]) is very cold and has very high 
pressure, high oxygen content, and low nutrient content. There are a variety 
of invertebrates and fishes found in this zone, but the abyssal zone does not 
have plants because of the lack of light. Hydrothermal vents are found 
primarily in the abyssal zone; chemosynthetic bacteria utilize the hydrogen 
sulfide and other minerals emitted from the vents as an energy source and 
serve as the base of the food chain found in the abyssal zone. 


Coral Reefs 


Coral reefs are ocean ridges formed by marine invertebrates living in warm 
shallow waters within the photic zone of the ocean. They are found within 
30° north and south of the equator. The Great Barrier Reef is a well-known 
reef system located several miles off the northeastern coast of Australia. 
Other coral reef systems are fringing islands, which are directly adjacent to 
land, or atolls, which are circular reef systems surrounding a former 
landmass that is now underwater. The coral organisms (members of phylum 
Cnidaria) are colonies of saltwater polyps that secrete a calcium carbonate 
skeleton. These calcium-rich skeletons slowly accumulate, forming the 
underwater reef ({link]). Corals found in shallower waters (at a depth of 
approximately 60 m or about 200 ft) have a mutualistic relationship with 
photosynthetic unicellular algae. The relationship provides corals with the 
majority of the nutrition and the energy they require. The waters in which 
these corals live are nutritionally poor and, without this mutualism, it would 
not be possible for large corals to grow. Some corals living in deeper and 
colder water do not have a mutualistic relationship with algae; these corals 
attain energy and nutrients using stinging cells on their tentacles to capture 


prey. 


It is estimated that more than 4,000 fish species inhabit coral reefs. These 
fishes can feed on coral, the cryptofauna (invertebrates found within the 
calcium carbonate substrate of the coral reefs), or the seaweed and algae 
that are associated with the coral. In addition, some fish species inhabit the 
boundaries of a coral reef; these species include predators, herbivores, or 


planktivores. Predators are animal species that hunt and are carnivores or 
“flesh eaters.” Herbivores eat plant material, and planktivores eat plankton. 


Coral reefs are formed by 
the calcium carbonate 
skeletons of coral 
organisms, which are 
marine invertebrates in 
the phylum Cnidaria. 
(credit: Terry Hughes) 


Note: 

Evolution Connection 

Global Decline of Coral Reefs 

It takes a long time to build a coral reef. The animals that create coral reefs 
have evolved over millions of years, continuing to slowly deposit the 


calcium carbonate that forms their characteristic ocean homes. Bathed in 
warm tropical waters, the coral animals and their symbiotic algal partners 
evolved to survive at the upper limit of ocean water temperature. 

Together, climate change and human activity pose dual threats to the long- 
term survival of the world’s coral reefs. As global warming due to fossil 
fuel emissions raises ocean temperatures, coral reefs are suffering. The 
excessive warmth causes the reefs to expel their symbiotic, food-producing 
algae, resulting in a phenomenon known as bleaching. When bleaching 
occurs, the reefs lose much of their characteristic color as the algae and the 
coral animals die if loss of the symbiotic zooxanthellae is prolonged. 
Rising levels of atmospheric carbon dioxide further threaten the corals in 
other ways; as CO, dissolves in ocean waters, it lowers the pH and 
increases ocean acidity. As acidity increases, it interferes with the 
calcification that normally occurs as coral animals build their calcium 
carbonate homes. 

When a coral reef begins to die, species diversity plummets as animals lose 
food and shelter. Coral reefs are also economically important tourist 
destinations, so the decline of coral reefs poses a serious threat to coastal 
economies. 

Human population growth has damaged corals in other ways, too. As 
human coastal populations increase, the runoff of sediment and agricultural 
chemicals has increased, too, causing some of the once-clear tropical 
waters to become cloudy. At the same time, overfishing of popular fish 
species has allowed the predator species that eat corals to go unchecked. 
Although a rise in global temperatures of 1—2°C (a conservative scientific 
projection) in the coming decades may not seem large, it is very significant 
to this biome. When change occurs rapidly, species can become extinct 
before evolution leads to new adaptations. Many scientists believe that 
global warming, with its rapid (in terms of evolutionary time) and 
inexorable increases in temperature, is tipping the balance beyond the point 
at which many of the world’s coral reefs can recover. 


Estuaries: Where the Ocean Meets Fresh Water 


Estuaries are biomes that occur where a source of fresh water, such as a 
river, meets the ocean. Therefore, both fresh water and salt water are found 
in the same vicinity; mixing results in a diluted (brackish) saltwater. 
Estuaries form protected areas where many of the young offspring of 
crustaceans, mollusks, and fish begin their lives. Salinity is a very important 
factor that influences the organisms and the adaptations of the organisms 
found in estuaries. The salinity of estuaries varies and is based on the rate of 
flow of its freshwater sources. Once or twice a day, high tides bring salt 
water into the estuary. Low tides occurring at the same frequency reverse 
the current of salt water. 


The short-term and rapid variation in salinity due to the mixing of fresh 
water and salt water is a difficult physiological challenge for the plants and 
animals that inhabit estuaries. Many estuarine plant species are halophytes: 
plants that can tolerate salty conditions. Halophytic plants are adapted to 
deal with the salinity resulting from saltwater on their roots or from sea 
spray. In some halophytes, filters in the roots remove the salt from the water 
that the plant absorbs. Animals, such as mussels and clams (phylum 
Mollusca), have developed behavioral adaptations that expend a lot of 
energy to function in this rapidly changing environment. When these 
animals are exposed to low salinity, they stop feeding, close their shells, and 
switch from aerobic respiration (in which they use gills) to anaerobic 
respiration (a process that does not require oxygen). When high tide returns 
to the estuary, the salinity and oxygen content of the water increases, and 
these animals open their shells, begin feeding, and return to aerobic 
respiration. 


Freshwater Biomes 


Freshwater biomes include lakes and ponds (standing water) as well as 
rivers and streams (flowing water). They also include wetlands, which will 
be discussed later. Humans rely on freshwater biomes to provide aquatic 
resources for drinking water, crop irrigation, sanitation, and industry. These 
various roles and human benefits are referred to as ecosystem services. 
Lakes and ponds are found in terrestrial landscapes and are, therefore, 
connected with abiotic and biotic factors influencing these terrestrial 
biomes. 


Lakes and Ponds 


Lakes and ponds can range in area from a few square meters to thousands 
of square kilometers. Temperature is an important abiotic factor affecting 
living things found in lakes and ponds. In the summer, thermal stratification 
of lakes and ponds occurs when the upper layer of water is warmed by the 
sun and does not mix with deeper, cooler water. Light can penetrate within 
the photic zone of the lake or pond. Phytoplankton (algae and 
cyanobacteria) are found here and carry out photosynthesis, providing the 
base of the food web of lakes and ponds. Zooplankton, such as rotifers and 
small crustaceans, consume these phytoplankton. At the bottom of lakes 
and ponds, bacteria in the aphotic zone break down dead organisms that 
sink to the bottom. 


Nitrogen and phosphorus are important limiting nutrients in lakes and 
ponds. Because of this, they are determining factors in the amount of 
phytoplankton growth in lakes and ponds. When there is a large input of 
nitrogen and phosphorus (from sewage and runoff from fertilized lawns and 
farms, for example), the growth of algae skyrockets, resulting in a large 
accumulation of algae called an algal bloom. Algal blooms ({link]) can 
become so extensive that they reduce light penetration in water. As a result, 
the lake or pond becomes aphotic and photosynthetic plants cannot survive. 
When the algae die and decompose, severe oxygen depletion of the water 
occurs. Fishes and other organisms that require oxygen are then more likely 
to die, and resulting dead zones are found across the globe. Lake Erie and 
the Gulf of Mexico represent freshwater and marine habitats where 
phosphorus control and storm water runoff pose significant environmental 
challenges. 


The uncontrolled growth of 
algae in this lake has resulted in 
an algal bloom. (credit: Jeremy 

Nettleton) 


Rivers and Streams 


Rivers and streams are continuously moving bodies of water that carry large 
amounts of water from the source, or headwater, to a lake or ocean. The 
largest rivers include the Nile River in Africa, the Amazon River in South 
America, and the Mississippi River in North America. 


Abiotic features of rivers and streams vary along the length of the river or 
stream. Streams begin at a point of origin referred to as source water. The 
source water is usually cold, low in nutrients, and clear. The channel (the 
width of the river or stream) is narrower than at any other place along the 
length of the river or stream. Because of this, the current is often faster here 
than at any other point of the river or stream. 


The fast-moving water results in minimal silt accumulation at the bottom of 
the river or stream; therefore, the water is clear. Photosynthesis here is 
mostly attributed to algae that are growing on rocks; the swift current 
inhibits the growth of phytoplankton. An additional input of energy can 


come from leaves or other organic material that falls into the river or stream 
from trees and other plants that border the water. When the leaves 
decompose, the organic material and nutrients in the leaves are returned to 
the water. Plants and animals have adapted to this fast-moving water. For 
instance, leeches (phylum Annelida) have elongated bodies and suckers on 
both ends. These suckers attach to the substrate, keeping the leech anchored 
in place. Freshwater trout species (phylum Chordata) are an important 
predator in these fast-moving rivers and streams. 


As the river or stream flows away from the source, the width of the channel 
gradually widens and the current slows. This slow-moving water, caused by 
the gradient decrease and the volume increase as tributaries unite, has more 
sedimentation. Phytoplankton can also be suspended in slow-moving water. 
Therefore, the water will not be as clear as it is near the source. The water is 
also warmer. Worms (phylum Annelida) and insects (phylum Arthropoda) 
can be found burrowing into the mud. The higher order predator vertebrates 
(phylum Chordata) include waterfowl, frogs, and fishes. These predators 
must find food in these slow moving, sometimes murky, waters and, unlike 
the trout in the waters at the source, these vertebrates may not be able to use 
vision as their primary sense to find food. Instead, they are more likely to 
use taste or chemical cues to find prey. 


Wetlands 


Wetlands are environments in which the soil is either permanently or 
periodically saturated with water. Wetlands are different from lakes because 
wetlands are shallow bodies of water whereas lakes vary in depth. Emergent 
vegetation consists of wetland plants that are rooted in the soil but have 
portions of leaves, stems, and flowers extending above the water’s surface. 
There are several types of wetlands including marshes, swamps, bogs, 
mudflats, and salt marshes ((link]). The three shared characteristics among 
these types—what makes them wetlands—are their hydrology, hydrophytic 
vegetation, and hydric soils. 


Located in southern Florida, 
Everglades National Park is vast 
array of wetland environments, 
including sawgrass marshes, 
cypress swamps, and estuarine 
mangrove forests. Here, a great 
egret walks among cypress 
trees. (credit: NPS) 


Freshwater marshes and swamps are characterized by slow and steady 
water flow. Bogs develop in depressions where water flow is low or 
nonexistent. Bogs usually occur in areas where there is a clay bottom with 
poor percolation. Percolation is the movement of water through the pores in 
the soil or rocks. The water found in a bog is stagnant and oxygen depleted 
because the oxygen that is used during the decomposition of organic matter 
is not replaced. As the oxygen in the water is depleted, decomposition 
slows. This leads to organic acids and other acids building up and lowering 
the pH of the water. At a lower pH, nitrogen becomes unavailable to plants. 
This creates a challenge for plants because nitrogen is an important limiting 
resource. Some types of bog plants (such as sundews, pitcher plants, and 
Venus flytraps) capture insects and extract the nitrogen from their bodies. 
Bogs have low net primary productivity because the water found in bogs 
has low levels of nitrogen and oxygen. 


Population 


"Anyone who believes in indefinite growth of anything physical on a 
physically finite planet is either a madman or an economist." Kenneth 
Boulding, economist (President Kennedy's Environmental Advisor 1966) 


In biology, a population is a very specific thing. A population is all the 
members of a species living within a specific area. Populations are typically 
dynamic entities. They expand and contract, but, as noted above, they 
cannot expand infinitely. Populations fluctuate based on a number of factors: 
seasonal and yearly changes in the environment, natural disasters such as 
forest fires and volcanic eruptions, competition for resources between and 
within species, and the amount of habitat (where an organism lives). The 
statistical study of population dynamics, demography, uses a series of 
mathematical tools to investigate how populations respond to changes in 
their biotic and abiotic environments. Many of these tools were originally 
designed to study human populations. For example, life tables, which detail 
the life expectancy of individuals within a population, were initially 
developed by life insurance companies to set insurance rates. In fact, while 
the term “demographics” is commonly used when discussing humans, all 
living populations can be studied using this approach. 


Population Size and Density 


The study of any population usually begins by determining how many 
individuals of a particular species exist, and how closely associated they are 
with each other. Within a particular habitat, a population can be 
characterized by its population size (N), the total number of individuals, 
and its population density, the number of individuals within a specific area 
or volume. Population size and density are the two main characteristics used 
to describe and understand populations. For example, populations with more 
individuals may be more stable than smaller populations based on their 
genetic variability, and thus their potential to adapt to the environment. 
Alternatively, a member of a population with low population density (more 
spread out in the habitat), might have more difficulty finding a mate to 
reproduce compared to a population of higher density. As is shown in [link], 
smaller organisms tend to be more densely distributed than larger organisms. 


Note: 


Relationship between Population and Body Mass in Australian Mammals 


Quoll 
Bandicoot 
Wombat 
Rat-kangaroo 
Potoroo 
Possom species 
Tree kangaroo 
Wallaby 
Kangaroo 
Bear cuscus 
Glider species 


Log density (km?) 


cI 
rT] 
a 
e 
K 
° 
a 
A 
fe) 
x 


2.0 3.0 
Log mass (grams) 


Australian mammals show a typical inverse 
relationship between population density and 
body size. 


Population Research Methods 


The most accurate way to determine population size is to simply count all of 
the individuals within the habitat. However, this method is often not 
logistically or economically feasible, especially when studying large 
habitats. Thus, scientists usually study populations by sampling a 
representative portion of each habitat and using these data to make 
inferences about the habitat as a whole. A variety of methods can be used to 
sample populations to determine their size and density. For immobile 
organisms such as plants, or for very small and slow-moving organisms, a 
quadrat may be used ([link]). A quadrat is a way of marking off square areas 
within a habitat, either by staking out an area with sticks and string, or by 
the use of a wood, plastic, or metal square placed on the ground. After 
setting the quadrats, researchers then count the number of individuals that lie 


within their boundaries. Multiple quadrat samples are performed throughout 
the habitat at several random locations. All of these data can then be used to 
estimate the population size and population density within the entire habitat. 
The number and size of quadrat samples depends on the type of organisms 
under study and other factors, including the density of the organism. For 
example, if sampling daffodils, a 1 m* quadrat might be used whereas with 
giant redwoods, which are larger and live much further apart from each 
other, a larger quadrat of 400 m* might be employed. This ensures that 
enough individuals of the species are counted to get an accurate sample that 
correlates with the habitat, including areas not sampled. 


A scientist uses a quadrat to 

measure population size and 

density. (credit: NPS Sonoran 
Desert Network) 


For mobile organisms, such as mammals, birds, or fish, a technique called 
mark and recapture is often used. This method involves marking a sample 
of captured animals in some way (such as tags, bands, paint, or other body 
markings), and then releasing them back into the environment to allow them 
to mix with the rest of the population; later, a new sample is collected, 
including some individuals that are marked (recaptures) and some 
individuals that are unmarked ({link]). 


Mark and recapture is used to measure the population 
size of mobile animals such as (a) bighorn sheep, (b) the 
California condor, and (c) salmon. (credit a: 
modification of work by Neal Herbert, NPS; credit b: 
modification of work by Pacific Southwest Region 
USFWS; credit c: modification of work by Ingrid 
Taylar) 


Using the ratio of marked and unmarked individuals, scientists determine 
how many individuals are in the sample. From this, calculations are used to 
estimate the total population size. This method assumes that the larger the 
population, the lower the percentage of tagged organisms that will be 
recaptured since they will have mixed with more untagged individuals. For 
example, if 80 deer are captured, tagged, and released into the forest, and 
later 100 deer are captured and 20 of them are already marked, we can 
determine the population size (N) using the following equation: 

Equation: 


(number marked first catch x total number of second catch) 


number marked second catch 
Using our example, the population size would be estimated at 400. 
Equation: 


(80 x 100) 
20 


= 400 


Therefore, there are an estimated 400 total individuals in the original 
population. 


There are some limitations to the mark and recapture method. Some animals 
from the first catch may learn to avoid capture in the second round, thus 
inflating population estimates. Alternatively, animals may preferentially be 
retrapped (especially if a food reward is offered), resulting in an 
underestimate of population size. Also, some species may be harmed by the 
marking technique, reducing their survival. A variety of other techniques 
have been developed, including the electronic tracking of animals tagged 
with radio transmitters and the use of data from commercial fishing and 
trapping operations to estimate the size and health of populations and 
communities. 


Species Distribution 


In addition to measuring simple density, further information about a 
population can be obtained by looking at the distribution of the individuals. 
Species dispersion patterns (or distribution patterns) show the spatial 
relationship between members of a population within a habitat at a particular 
point in time. In other words, they show whether members of the species 
live close together or far apart, and what patterns are evident when they are 
spaced apart. 


Individuals in a population can be more or less equally spaced apart, 
dispersed randomly with no predictable pattern, or clustered in groups. 
These are known as uniform, random, and clumped dispersion patterns, 
respectively ({link]). Uniform dispersion is observed in plants that secrete 
substances inhibiting the growth of nearby individuals (such as the release 
of toxic chemicals by the sage plant Salvia leucophylla, a phenomenon 
called allelopathy or plants in arid habitats that compete intensely for limited 
soil water and nutrients.) and in animals like the penguin that maintain a 
defined territory. An example of random dispersion occurs with dandelion 
and other plants that have wind-dispersed seeds that germinate wherever 
they happen to fall in a favorable environment. A clumped dispersion may 
be seen in plants that drop their seeds straight to the ground, such as oak 
trees, or animals that live in groups (schools of fish or herds of elephants). 


Clumped dispersions may also be a function of habitat heterogeneity. Thus, 
the dispersion of the individuals within a population provides more 
information about how they interact with each other than does a simple 
density measurement. Just as lower density species might have more 
difficulty finding a mate, solitary species with a random distribution might 
have a similar difficulty when compared to social species clumped together 
in groups. 


Uniform Random Clumped 


Species may have uniform, random, or clumped distribution. 
Territorial birds such as penguins tend to have uniform 
distribution. Plants such as dandelions with wind-dispersed 
seeds tend to be randomly distributed. Animals such as 
elephants that travel in groups exhibit clumped distribution. 
(credit a: modification of work by Ben Tubby; credit b: 
modification of work by Rosendahl; credit c: modification of 
work by Rebecca Wood) 


Demography 


While population size and density describe a population at one particular 
point in time, scientists must use demography to study the dynamics of a 
population. Demography is the statistical study of population changes over 
time: birth rates, death rates, migration and life expectancies. Each of these 
measures, especially birth rates, may be affected by the population 


characteristics described above. For example, a large population size results 
in a higher birth rate because more potentially reproductive individuals are 
present. In contrast, a large population size can also result in a higher death 
rate because of competition, disease, and the accumulation of waste. 
Similarly, a higher population density or a clumped dispersion pattern 
results in more potential reproductive encounters between individuals, 
which can increase birth rate. Migration the movement of individuals into a 
population (immigration) and out of a population (emigration) can 
drastically influence population growth, especially the colonization of new 
areas. Lastly, a female-biased sex ratio (the ratio of males to females) or age 
structure (the proportion of population members at specific age ranges) 
composed of many individuals of reproductive age can increase birth rates. 


In addition, the demographic characteristics of a population can influence 
how the population grows or declines over time. If birth and death rates are 
equal, the population remains stable. However, the population size will 
increase if birth rates exceed death rates; the population will decrease if birth 
rates are less than death rates. Life expectancy is another important factor; 
the length of time individuals remain in the population impacts local 
resources, reproduction, and the overall health of the population. These 
demographic characteristics are often displayed in the form of a life table. 


Life Tables 


Life tables provide important information about the life history of an 
organism. Life tables divide the population into age groups and often sexes, 
and show how long a member of that group is likely to live. They are 
modeled after actuarial tables used by the insurance industry for estimating 
human life expectancy. Life tables may include the probability of 
individuals dying before their next birthday (i.e., their mortality rate, the 
percentage of surviving individuals dying at a particular age interval, and 
their life expectancy at each interval. An example of a life table is shown in 
[link] from a study of Dall mountain sheep, a species native to northwestern 
North America. Notice that the population is divided into age intervals 
(column A). The mortality rate (per 1000), shown in column D, is based on 
the number of individuals dying during the age interval (column B) divided 


by the number of individuals surviving at the beginning of the interval 
(Column C), multiplied by 1000. 
Equation: 


number of individuals dying 


mortality rate = x 1000 


number of individuals surviving 


For example, between ages three and four, 12 individuals die out of the 776 
that were remaining from the original 1000 sheep. This number is then 
multiplied by 1000 to get the mortality rate per thousand. 

Equation: 


12 
tality rate = —-~ xl ew 15. 
mortality rate 776 * 000 5.0 


As can be seen from the mortality rate data (column D), a high death rate 
occurred when the sheep were between 6 and 12 months old, and then 
increased even more from 8 to 12 years old, after which there were few 
survivors. The data indicate that if a sheep in this population were to survive 
to age one, it could be expected to live another 7.7 years on average, as 
shown by the life expectancy numbers in column E. 


Life Table of Dall Mountain Sheep!2o™«! 

Data Adapted from Edward S. Deevey, Jr., “Life Tables for Natural 
Populations of Animals,” The Quarterly Review of Biology 22, no. 4 
(December 1947): 283-314. 


Age 
interval 
(years) 


0-0.5 
0.5-1 
1-2 
23 
3-4 
4-5 


5-6 


Number 
dying in 
age 
interval 
out of 
1000 
born 

54 

145 

12 

13 

12 

30 

46 

48 

69 

132 

187 

156 


90 


Number 
surviving 
at 
beginning 
of age 
interval 
out of 
1000 
born 
1000 
946 

801 

789 

776 

764 

734 

688 

640 

571 

439 

252 


96 


Mortality 
rate per 
1000 alive 
at 
beginning 
of age 
interval 
54.0 

153.3 

15.0 

16.5 

15.5 

39.3 

62.7 

69.8 

107.8 
231.2 
426.0 
619.0 


907.0 


Life 
expectancy 
or mean 
lifetime 
remaining 
to those 
attaining 
age 
interval 


7.06 


12-13 3 6 500.0 i2 
13-14 3 3 1000 0.7 


This life table of Ovis dalli shows the number of deaths, number of survivors, 
mortality rate, and life expectancy at each age interval for the Dall mountain 
sheep. 


Survivorship Curves 


Another tool used by population ecologists is a survivorship curve, which 
is a graph of the number of individuals surviving at each age interval plotted 
versus time (usually with data compiled from a life table). These curves 
allow us to compare the life histories of different populations ((link]). 
Humans and most primates exhibit a Type I survivorship curve because a 
high percentage of offspring survive their early and middle years—death 
occurs predominantly in older individuals. These types of species usually 
have small numbers of offspring at one time, and they give a high amount of 
parental care to them to ensure their survival. Birds and perennial 
herbaceous plants are examples of an intermediate of Type II survivorship 
curve because the probability of death is equal for all age classes in these 
organisms. Some of the animals also may have relatively few offspring and 
provide significant parental care. Trees, marine invertebrates, and most 
fishes exhibit a Type III survivorship curve because very few of these 
organisms survive their younger years; however, those that make it to an old 
age are more likely to survive for a relatively long period of time. 
Organisms in this category usually have a very large number of offspring, 
but once they are born, little parental care is provided. Thus these offspring 
are “on their own” and vulnerable to predation, but their sheer numbers 
assure the survival of enough individuals to perpetuate the species. 


Survivorship Curve 


Type | (humans) { 


Type Ill (trees) 


~~ 
2 
® 
3) 
a 
D> 
aS} 
= 
> 
£& 
2 
2 
5 
a 
wo 
i 
3 
3 
2 
3 
£ 
re 
S 
has 
o 
2 
E 
5 
2 


jo) 


50 
Percentage of maximum life expectancy 


Survivorship curves show the 
distribution of individuals in 
a population according to 
age. Humans and most 
mammals have a Type I 
survivorship curve because 
death primarily occurs in the 
older years. Birds have a 
Type II survivorship curve, as 
death at any age is equally 
probable. Trees have a Type 
II survivorship curve 
because very few survive the 
younger years, but after a 
certain age, individuals are 
much more likely to survive. 


Population Growth 


"The greatest shortcoming of the human race is our inability to understand 
the exponential function." - Dr. Albert A. Bartlett, Emeritus Professor of 
Physics, University of Colorado 


Exponential Growth 


Charles Darwin, in his theory of evolution by natural selection, was greatly 
influenced by the English clergyman Thomas Malthus. Malthus published a 
book in 1798 stating that populations with unlimited natural resources grow 
very rapidly. This accelerating pattern of increasing population size is called 
exponential growth. 


The best example of exponential growth is seen in bacteria. Bacteria can 
undergo cell division about every hour. If 1000 bacteria are placed in a large 
flask with an unlimited supply of nutrients (so the nutrients will not become 
depleted), after an hour, there is one round of division, resulting in 2000 
organisms—an increase of 1000. In another hour, each of the 2000 
organisms will double, producing 4000, an increase of 2000 organisms. 
After the third hour, there should be 8000 bacteria in the flask, an increase 
of 4000 organisms. The important concept of exponential growth is that 
population growth (G)—the number of organisms added in each 
reproductive generation—is accelerating; that is, it is increasing at a greater 
and greater rate. After 1 day and 24 of these cycles, the population would 
have increased from 1000 to more than 16 billion. When the population 
size, N, is plotted over time, a J-shaped growth curve is produced ([link]). 


The bacteria example is not representative of the real world where resources 
are limited. Furthermore, some bacteria will die during the experiment and 
thus not reproduce, lowering the growth rate. Therefore, when calculating 
the growth of a population, the number of deaths (D (number organisms 
that die during a particular time interval) is subtracted from the number of 
births (B) (number organisms that are born during that interval). This is 
shown in the following formula: 

Equation: 


G(population growth) = B (births) - D (deaths) 


Now let's examine how the average number of births and deaths relate to 
population growth. The average birth and death rates based on the number 
of individuals in a population is on a per capita basis. So, the per capita 
birth rate (b) is the number of births during a time interval divided by the 
number of individuals in the population at that time, and the per capita 
death rate (d) is the number of deaths during a time interval divided by the 
number of individuals in the population at that time. See the equations 
below for a simple formula. 

Equation: 


B(number of births) 


b a Dit £AVG | ee 
(per capita birth rate) N (total number of individuals) 


Equation: 


D(number of deaths) 


d iba death tate ) Seg 
(per capita death rate) =— (total number of individuals) 


Now returning to the simple population growth equation above, we can 
convert this simple model to one in which births and deaths are expressed 
on a per capita basis for a time interval. Thus, B (births) = bN (the per 
capita birth rate “b” multiplied by the number of individuals “N”) and D 
(deaths) =dN (the per capita death rate “d” multiplied by the number of 
individuals “N”). When substituting bN for B and dN for D in simple 
growth equation, we can examine the population growth rate based on per 
capita birth and death rates as seen the equation below. 

Equation: 


G=bN — dN 


The above equation can be simplified to the following. 
Equation: 


G=(b —d)N 


Now, the difference between per capita birth rate and per capita death rates 
is further simplified by substituting the term “r” (per capita growth rate). 
So, the per capita growth rate (r) is equal to the per capita birth rate (b) 
minus the per capita death rate (d), or r = b - d. 

Equation: 


G=rN 


The value “r” can be positive, meaning the population is increasing in size; 
or negative, meaning the population is decreasing in size; or zero, where the 
population’s size is unchanging, a condition known as zero population 
growth. A further refinement of the formula recognizes that different 
species have inherent differences in their per capita growth rate (often 
thought of as the potential for reproduction), even under ideal conditions. 
Obviously, a bacterium can reproduce more rapidly and have a higher per 
capita growth rate than a human. The maximal growth rate for a species is 
its biotic potential. 


Other factors that influence population growth (G) 


When calculating per capita growth rate (r) as above, we are referring to a 
closed system where individuals from other populations are not moving in 
and individuals are not leaving. Immigration and emigration are two more 
factors that can influence the growth of a population. Immigration is the 
movement of individuals into a population which adds individuals to the 
population, and emigration is the movement of individuals out of a 
population which removes individuals to a population. So, the rates of 
immigration and emigration are two other factors population biologists need 
to consider when describing population growth (G). 


o o 
AN N 
n 2) 
i= c 
Ss S 
i & 
= = 
s s 
a a 


When resources are unlimited, populations exhibit 
exponential growth, resulting in a J-shaped curve. 
When resources are limited, populations exhibit 
logistic growth. In logistic growth, population 
expansion decreases as resources become scarce, and 
it levels off when the carrying capacity of the 
environment is reached, resulting in an S-shaped 
curve. 


Logistic Growth 


Exponential growth is possible only when natural resources are not limited. 
This occurs only infrequently and briefly in nature, such as when a 
population colonizes a new habitat or is recovering from a major 
disturbance. Charles Darwin recognized this fact in his description of the 
“struggle for existence,” which states that individuals will compete (with 
members of their own or other species) for limited resources. The 
successful ones will survive to pass on their own characteristics and traits 
(which we know now are transferred by genes) to the next generation at a 
greater rate (natural selection). To model the reality of limited resources, 
population ecologists developed the logistic growth model. 


Carrying Capacity and the Logistic Model 


In the real world, with its limited resources, exponential growth cannot 
continue indefinitely. Exponential growth may occur in environments where 
there are few individuals and plentiful resources, but when the number of 
individuals gets large enough, resources will be depleted, slowing the 
growth rate. Eventually, the growth rate will plateau or level off ((link]). 
This population size, which represents the maximum population size that a 
particular environment can support, is called the carrying capacity, or K. 


The formula we use to calculate logistic growth adds the carrying capacity 
as a moderating force in the growth rate. The expression “K — N” divided by 
“K” is the fraction of the carrying capacity available for further growth. 
Thus, the exponential growth model is restricted by this factor to generate 
the logistic growth equation: 

Equation: 


(K — N) 


Gann 
7 K 


Notice that when N is very small, (K-N)/K becomes close to K/K or 1, and 
the right side of the equation reduces to rN, which means the population is 
growing exponentially and is not influenced by carrying capacity. On the 
other hand, when N is large, (K-N)/K comes close to zero, which means that 
population growth will be slowed greatly or even stopped. Thus, population 
growth is greatly slowed when the population size is close to the carrying 
capacity. This model also allows for negative population growth, or a 
population decline. This occurs when the number of individuals in the 
population exceeds the carrying capacity (because the value of (K-N)/K is 
negative). 


A graph of this equation yields an S-shaped curve ([link]), and it is a more 
realistic model of population growth than exponential growth. There are 
three different sections to an S-shaped curve. Initially, growth is exponential 
because there are few individuals and ample resources available. Then, as 
resources begin to become limited, the growth rate decreases. Finally, 
growth levels off at the carrying capacity of the environment, with little 
change in population size over time. 


Role of Intraspecific Competition 


The logistic model assumes that every individual within a population will 
have equal access to resources and, thus, an equal chance for survival. For 
plants, the amount of water, sunlight, nutrients, and the space to grow are 
the important resources, whereas in animals, important resources may 
include food, water, shelter, nesting space, and mates. 


In the real world, variation in a trait among individuals within a population 
means that some individuals will be better adapted to their environment 
than others. The resulting competition between population members of the 
Same species for resources is termed intraspecific competition (intra- = 
“within”; -specific = “species”). Intraspecific competition for resources may 
not affect populations that are well below their carrying capacity— 
resources are plentiful and all individuals can obtain what they need. 
However, as population size increases, this competition intensifies. In 
addition, the accumulation of waste products can reduce an environment’s 
Carrying capacity. 


Examples of Logistic Growth 


Yeast, a microscopic fungus used to make bread and alcoholic beverages, 
exhibits the classical S-shaped curve when grown in a test tube ([Link]a). Its 
growth levels off as the population depletes the nutrients that are necessary 
for its growth. However, there are variations to this idealized curve. 
Examples in wild populations include sheep and harbor seals ({link]b). In 
both examples, the population size exceeds the carrying capacity for short 
periods of time and then falls below the carrying capacity afterwards. This 
fluctuation in population size continues to occur as the population oscillates 
around its carrying capacity. Still, even with this oscillation, the logistic 
model is still widely supported. 


Note: 


ry 
N 


g 
ES 
a) 
= 8 
IE 
s 
° 
[= 
<x 


3 


g 


288 8 8 


1980 1990 1995 2000 


(b) 


(a) Yeast grown in ideal conditions in a test tube show a 
classical S-shaped logistic growth curve, whereas (b) a 
natural population of seals shows real-world fluctuation. 


Population Regulation 


"If we don't halt population growth with justice and compassion, it will be 
done for us by nature, brutally and without pity- and will leave a ravaged 
world." - Dr. Henry W. Kendall, Nobel Laureate in Physics, 1990 


The natural mechanisms regulating population growth can indeed be brutal. 
Carrying capacity is a mathematical sanitization of the realities of famine, 
disease, and other causes of death. And the logistic model of population 
growth, while valid in many natural populations and a useful model, is a 
simplification of real-world population dynamics. Implicit in the model is 
that the carrying capacity of the environment does not change, which is not 
the case. The carrying capacity varies annually: for example, some 
summers are hot and dry whereas others are cold and wet. In many areas, 
the carrying capacity during the winter is much lower than it is during the 
summer. Also, natural events such as earthquakes, volcanoes, and fires can 
alter an environment and hence its carrying capacity. Additionally, 
populations do not usually exist in isolation. They engage in interspecific 
competition: that is, they share the environment with other species, 
competing with them for the same resources. These factors are also 
important to understanding how a specific population will grow. 


Nature regulates population growth in a variety of ways. These are grouped 
into density-dependent factors, in which the density of the population at a 
given time affects growth rate and mortality, and density-independent 
factors, which influence mortality in a population regardless of population 
density. Note that in the former, the effect of the factor on the population 
depends on the density of the population at onset. Conservation biologists 
want to understand both types because this helps them manage populations 
and prevent extinction or overpopulation. 


Density-dependent Regulation 


Most density-dependent factors are biological in nature (biotic), and include 
predation, inter- and intraspecific competition, accumulation of waste, and 

diseases such as those caused by parasites. Usually, the denser a population 
is, the greater its mortality rate. For example, during intra- and interspecific 


competition, the reproductive rates of the individuals will usually be lower 
and mortality rates higher, reducing their population’s rate of growth. In 
addition, low prey density increases the mortality of its predator because it 
has more difficulty locating its food source. 


An example of density-dependent regulation is shown in [link] with results 
from a study focusing on the giant intestinal roundworm (Ascaris 
lumbricoides), a parasite of humans and other mammals.!{2™te] Denser 
populations of the parasite exhibited lower fecundity: they contained fewer 
eggs. One possible explanation for this is that females would be smaller in 
more dense populations (due to limited resources) and that smaller females 
would have fewer eggs. This hypothesis was tested and disproved in a 2009 
study which showed that female weight had no influence. !{2o™2te! The actual 
cause of the density-dependence of fecundity in this organism is still 
unclear and awaiting further investigation. 

N.A. Croll et al., “The Population Biology and Control of Ascaris 
lumbricoides in a Rural Community in Iran.” Transactions of the Royal 
Society of Tropical Medicine and Hygiene 76, no. 2 (1982): 187-197, 
doi:10.1016/0035-9203(82)90272-3. 

Martin Walker et al., “Density-Dependent Effects on the Weight of Female 
Ascaris lumbricoides Infections of Humans and its Impact on Patterns of 
Egg Production.” Parasites & Vectors 2, no. 11 (February 2009), 
doi:10.1186/1756-3305-2-11. 


Fecundity as a Function of Population 


2 
oc 
£ 
o 
2 
— 
o 
2 
12) 
a 
a 
o 
- 
) 
= 
o 
2 
£ 
=] 
z 


20 30 
Number of worms 


In this population of roundworms, 


fecundity (number of eggs) 
decreases with population density. 
[footnote] 

N.A. Croll et al., “The Population 
Biology and Control of Ascaris 
lumbricoides in a Rural 
Community in Iran.” Transactions 
of the Royal Society of Tropical 
Medicine and Hygiene 76, no. 2 
(1982): 187-197, 
doi:10.1016/0035-9203(82)90272- 
2: 


Density-independent Regulation and Interaction with Density- 
dependent Factors 


Many factors, typically physical or chemical in nature (abiotic), influence 
the mortality of a population regardless of its density, including weather, 
natural disasters, and pollution. An individual deer may be killed in a forest 
fire regardless of how many deer happen to be in that area. Its chances of 
survival are the same whether the population density is high or low. The 
same holds true for cold winter weather. 


In real-life situations, population regulation is very complicated and 
density-dependent and independent factors can interact. A dense population 
that is reduced in a density-independent manner by some environmental 
factor(s) will be able to recover differently than a sparse population. For 
example, a population of deer affected by a harsh winter will recover faster 
if there are more deer remaining to reproduce. 


Note: 
Evolution Connection 
Why Did the Woolly Mammoth Go Extinct? 


The three photos include: (a) 1916 mural of a mammoth 
herd from the American Museum of Natural History, (b) 
the only stuffed mammoth in the world, from the 
Museum of Zoology located in St. Petersburg, Russia, 
and (c) a one-month-old baby mammoth, named Lyuba, 
discovered in Siberia in 2007. (credit a: modification of 
work by Charles R. Knight; credit b: modification of 
work by “Tanapon”/Flickr; credit c: modification of 
work by Matt Howry) 


It's easy to get lost in the discussion of dinosaurs and theories about why 
they went extinct 65 million years ago. Was it due to a meteor slamming 
into Earth near the coast of modern-day Mexico, or was it from some long- 
term weather cycle that is not yet understood? One hypothesis that will 
never be proposed is that humans had something to do with it. Mammals 
were small, insignificant creatures of the forest 65 million years ago, and 
no humans existed. 

Woolly mammoths, however, began to go extinct about 10,000 years ago, 
when they shared the Earth with humans who were no different 
anatomically than humans today ([link]). Mammoths survived in isolated 
island populations as recently as 1700 BC. We know a lot about these 
animals from carcasses found frozen in the ice of Siberia and other regions 
of the north. Scientists have sequenced at least 50 percent of its genome 
and believe mammoths are between 98 and 99 percent identical to modern 
elephants. 

It is commonly thought that climate change and human hunting led to their 
extinction. A 2008 study estimated that climate change reduced the 
mammoth’s range from 3,000,000 square miles 42,000 years ago to 
310,000 square miles 6,000 years ago. f20™motel Tt is also well documented 
that humans hunted these animals. A 2012 study showed that no single 
factor was exclusively responsible for the extinction of these magnificent 


creatures, |!0otmote] Ty addition to human hunting, climate change, and 
reduction of habitat, these scientists demonstrated another important factor 
in the mammoth’s extinction was the migration of humans across the 
Bering Strait to North America during the last ice age 20,000 years ago. 
David Nogués-Bravo et al., “Climate Change, Humans, and the Extinction 
of the Woolly Mammoth.” PLoS Biol 6 (April 2008): e79, 
doi:10.1371/journal.pbio.0060079. 

G.M. MacDonald et al., “Pattern of Extinction of the Woolly Mammoth in 
Beringia.” Nature Communications 3, no. 893 (June 2012), 
doi:10.1038/ncomms1881. 

The maintenance of stable populations was and is very complex, with 
many interacting factors determining the outcome. It is important to 
remember that humans are also part of nature. Once we contributed to a 
species’ decline using primitive hunting technology only. 


Human Population Growth 


"Unlike plagues of the dark ages or contemporary diseases we do not 
understand, the moder plague of overpopulation is soluble by means we 
have discovered and with resources we possess. What is lacking is not 
sufficient knowledge of the solution but universal consciousness of the 
gravity of the problem and education of the billions who are its victim." - 
Martin Luther King, Jr., civil rights leader and Nobel laureate 


Concepts of animal population dynamics can be applied to human 
population growth. Humans are not unique in their ability to alter their 
environment. For example, beaver dams alter the stream environment where 
they are built. Humans, however, have the ability to alter their environment 
to increase its carrying capacity sometimes to the detriment of other species 
(e.g., via artificial selection for crops that have a higher yield). Earth’s 
human population is growing rapidly, to the extent that some worry about 
the ability of the earth’s environment to sustain this population, as long- 
term exponential growth carries the potential risks of famine, disease, and 
large-scale death. 


Although humans have increased the carrying capacity of their 
environment, the technologies used to achieve this transformation have 
caused unprecedented changes to Earth’s environment, altering ecosystems 
to the point where some may be in danger of collapse. The depletion of the 
ozone layer, erosion due to acid rain, and damage from global climate 
change are caused by human activities. The ultimate effect of these changes 
on our carrying capacity is unknown. As some point out, it is likely that the 
negative effects of increasing carrying capacity will outweigh the positive 
ones—the carrying capacity of the world for human beings might actually 
decrease. 


The world’s human population is currently experiencing exponential growth 
even though human reproduction is far below its biotic potential ((link]). To 
reach its biotic potential, all females would have to become pregnant every 
nine months or so during their reproductive years. Also, resources would 
have to be such that the environment would support such growth. Neither of 
these two conditions exists. In spite of this fact, human population is still 
growing exponentially. 


=— World 
=— Africa 
~~ Asia 
~~ Europe 
3,000,000 == Latin America 
= Northern America 


5,000,000 


- 
(2) 
no] 
c 
© 
n 
J 
° 
<= 
£ 
£ 
& 
c 
2 
8 
] 
a 
f°) 
a 
sc 
£ 
i 
g 
a 
Ww 


&, ° 


Human population growth since 1000 AD is 
exponential (dark blue line). Notice that while 
the population in Asia (yellow line), which has 
many economically underdeveloped countries, 

is increasing exponentially, the population in 

Europe (light blue line), where most of the 
countries are economically developed, is 
growing much more slowly. 


A consequence of exponential human population growth is the time that it 
takes to add a particular number of humans to the Earth is becoming 
shorter. [link] shows that 130 years were necessary to add 1 billion humans 
in 1930, but it only took 24 years to add two billion people between 1975 
and 1999. As already discussed, at some point it would appear that our 
ability to increase our carrying capacity indefinitely on a finite world is 
uncertain. Without new technological advances, the human growth rate has 
been predicted to slow in the coming decades. However, the population will 
still be increasing and the threat of overpopulation remains. 


Time between Billions in World Population Growth 


1 billion: 1800 
2 billion: 1930 
3 billion: 1960 
4 billion: 1975 
5 billion: 1987 
6 billion: 1999 
7 billion: 2012 
8 billion: 2028 
9 billion: 2054 


Years 


Source: Population Reference Bureau 


The time between the addition of each billion human 
beings to Earth decreases over time. (credit: 
modification of work by Ryan T. Cragun) 


Overcoming Density-Dependent Regulation 


Humans are unique in their ability to alter their environment with the 
conscious purpose of increasing its carrying capacity. This ability is a major 
factor responsible for human population growth and a way of overcoming 
density-dependent growth regulation. Much of this ability is related to 
human intelligence, society, and communication. Humans can construct 
shelter to protect them from the elements and have developed agriculture 
and domesticated animals to increase their food supplies. In addition, 
humans use language to communicate this technology to new generations, 
allowing them to improve upon previous accomplishments. 


Other factors in human population growth are migration and public health. 
Humans originated in Africa, but have since migrated to nearly all 
inhabitable land on the Earth. Public health, sanitation, and the use of 
antibiotics and vaccines have decreased the ability of infectious disease to 
limit human population growth. In the past, diseases such as the bubonic 


plaque of the fourteenth century killed between 30 and 60 percent of 
Europe’s population and reduced the overall world population by as many 
as 100 million people. Today, the threat of infectious disease, while not 
gone, is certainly less severe. According to the World Health Organization, 
global death from infectious disease declined from 16.4 million in 1993 to 
14.7 million in 1992. To compare to some of the epidemics of the past, the 
percentage of the world's population killed between 1993 and 2002 
decreased from 0.30 percent of the world's population to 0.24 percent. Thus, 
it appears that the influence of infectious disease on human population 
growth is becoming less significant. 


Age Structure, Population Growth, and Economic 
Development 


The age structure of a population is an important factor in population 
dynamics. Age structure is the proportion of a population at different age 
ranges. Age structure allows better prediction of population growth, plus 
the ability to associate this growth with the level of economic development 
in the region. Countries with rapid growth have a pyramidal shape in their 
age structure diagrams, showing a preponderance of younger individuals, 
many of whom are of reproductive age or will be soon ((link]). This pattern 
is most often observed in underdeveloped countries where individuals do 
not live to old age because of less-than-optimal living conditions. Age 
structures of areas with slow growth, including developed countries such as 
the United States, have a parabola shape structure (stage 3) ([link]), with 
many fewer young and reproductive-aged individuals and a greater 
proportion of older individuals. Other developed countries, such as Italy, 
have zero population growth. The age structure of these populations is more 
conical, with an even greater percentage of middle-aged and older 
individuals. The actual growth rates in different countries are shown in 
[link], with the highest rates tending to be in the less economically 
developed countries of Africa and Asia. Lastly, both fertility rates and age 
structure interact to influence population growth rates. High fertility rates 
can increase population growth because more offspring are produced per 
individual, whereas a pyramid-like age structure increases growth rates 
because more individuals in the population are producing offspring. 


Age Structure Diagrams 


Stage 1: Rapid growth Stage 2: Slow growth Stage 3: Stable Stage 4: ? 


Typical age structure diagrams are shown. The rapid 
growth diagram narrows to a point, indicating that the 
number of individuals decreases rapidly with age. In the 
slow growth model, the number of individuals decreases 
steadily with age. Stable population diagrams are 
rounded on the top, showing that the number of 
individuals per age group decreases gradually, and then 
increases for the older part of the population. 


Age structure diagrams for rapidly growing, slow growing and stable 
populations are shown in stages 1 through 3. What type of population 
change do you think stage 4 represents? If you guessed decreasing, you are 
correct. 


Percent Growth in Population 
M-0% —0%-1% 1% Ff 2% [] 3%+ 


The percent growth rate of population in different countries is 
shown. Notice that the highest growth is occurring in less 
economically developed countries in Africa and Asia. 


Long-Term Consequences of Exponential Human Population 
Growth 


Many dire predictions have been made about the world’s population leading 
to a major crisis called the “population explosion.” In the 1968 book The 
Population Bomb, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed 
all of humanity is over. In the 1970s hundreds of millions of people will 
starve to death in spite of any crash programs embarked upon now. At this 
late date nothing can prevent a substantial increase in the world death 

rate.” oolnote] While many critics view this statement as an exaggeration, the 
laws of exponential population growth are still in effect, and unchecked 
human population growth cannot continue indefinitely. 

Paul R. Erlich, prologue to The Population Bomb, (1968; repr., New York: 
Ballantine, 1970). 


Efforts to control population growth led to the one-child policy in China, 
which used to include severe penalties for having more than 1 child. The 
policy itself, its social impacts, and the effectiveness of limiting overall 
population growth are controversial. In 2016, the Chinese government 
abolished the policy citing issues with age demography and sex ratios. In 
spite of population control policies, the human population continues to 
grow. At some point the food supply may run out because of the subsequent 
need to produce more and more food to feed our population. The United 
Nations estimates that future world population growth may vary from 6 
billion (a decrease) to 16 billion people by the year 2100. There is no way 
to know whether human population growth will moderate to the point 
where the crisis described by Dr. Ehrlich will be averted. 


Another result of population growth is the endangerment of the natural 
environment. Many countries have attempted to reduce the human impact 
on climate change by reducing their emission of the greenhouse gas carbon 


dioxide. However, these treaties have not been ratified by every country, 
and many underdeveloped countries trying to improve their economic 
condition may be less likely to agree with such provisions if it means 
slower economic development. Furthermore, the role of human activity in 
causing climate change has become a hotly debated socio-political issue in 
some developed countries, including the United States. Thus, we enter the 
future with considerable uncertainty about our ability to curb human 
population growth and protect our environment. 


Community Ecology 


"The outstanding scientific discovery of the twentieth century is not 
television, or radio, but rather the complexity of the land organism. Only 
those who know the most about it can appreciate how little we know about 
it. The last word in ignorance is the man who says of an animal or plant: 
"What good is it?" If the land mechanism as a whole is good, then every 
part is good, whether we understand it or not." - Aldo Leopold, A Sand 
County Almanac 


Populations rarely, if ever, live in isolation from populations of other 
species. In most cases, numerous species share a habitat. The interactions 
between these populations play a major role in regulating population 
growth and abundance. All populations occupying the same habitat form a 
community: all populations inhabiting a specific area at the same time. The 
number of species occupying the same habitat and their relative abundance 
is known as species diversity. Areas with low diversity, such as the glaciers 
of Antarctica, still contain a wide variety of living things, whereas the 
diversity of tropical rainforests is so great that it cannot be counted. 
Ecology is studied at the community level to understand how species 
interact with each other and what processes determine the patterns of 
species coexistence, diversity, and distributions that we see in nature Any 
interactions between two or more species is referred to globally as 
interspecific interactions , and there are specific terms for some of unique 
interactions that will be discussed throughout this section. These unique 
interactions can have a positive effect (+), a negative effect (-) or a neutral 
effect (0) for the individual of the species. 


Niche 


In a community, no two species can have exactly the same ecological 
requirement and persist together in equilibrium. In order for a species to 
survive in an area, to obtain nutrients and energy and to avoid predators, a 
certain combination of ecological variables are necessary. These ecological 
variables include the resources available (light, nutrients, food and habitat), 
environmental characteristics (temperature and water availability) and the 
interactions with other organisms. These ecological requirements and 


interactions are used to define an organisms niche. For example, the Black- 
tailed Prairie Dog (Cynomys ludovicianus ) [link] is mostly found in short 
grass prairie. They can live within a broad range of temperature and 
moisture, specific soil types, and forage on specific species of grasses. 
These characteristics, other variables and interspecific interactions define 
their niche. 

Black-Tailed Prairie Dog 


The Black-tailed Prairie Dog has a 
unique niche. They eat grass and 
are eaten by coyotes, black-footed 
ferrets and other carnivores. The 
prairie dog lives in burrows and 
this activity produces bare soil 
areas where seeds can germinate 
without being shaded by trees. The 
burrows once abandoned provide 
nesting sites for burrowing owls. 
(photo by D. A. Rintoul) 


Predation and Herbivory 


Perhaps the classical example of species interaction is predation: the 
hunting of prey by its predator where the predator is positively affected (+) 
and the prey is negatively affected (-). Nature shows on television highlight 
the drama of one living organism killing another. Populations of predators 
and prey in a community are not constant over time: in most cases, they 
vary in cycles that appear to be related. The most often cited example of 
predator-prey dynamics is seen in the cycling of the lynx (predator) and the 
snowshoe hare (prey), using nearly 200 year-old trapping data from North 
American forests ([link]). This cycle of predator and prey repeats itself 
approximately every 10 years, with the predator population lagging 1—2 
years behind that of the prey population. As the hare numbers increase, 
there is more food available for the lynx, allowing the lynx population to 
increase as well. When the lynx population grows to a threshold level, 
however, they kill so many hares that hare population begins to decline, 
followed by a decline in the lynx population because of scarcity of food. 
When the lynx population is low, the hare population size begins to increase 
due, at least in part, to low predation pressure, starting the cycle anew. 


Predator-prey Dynamics 


[Hare (red) 
|_| Lynx (blue) 


Thousands of animals 


1845 1865 1885 1905 1925 
Time (years) 


The cycling of lynx and snowshoe hare 
populations in Northern Ontario is an example 
of predator-prey dynamics. 


The idea that the population cycling of the two species is entirely controlled 
by predation models has come under question. More recent studies have 
pointed to undefined density-dependent factors as being important in the 
cycling, in addition to predation. One possibility is that the cycling is 
inherent in the hare population due to density-dependent effects such as 
lower fecundity (maternal stress) caused by crowding when the hare 
population gets too dense. The hare cycling would then induce the cycling 
of the lynx because it is the lynxes’ major food source. In addition, many 
populations of annual plants show periodic cycles that are completely 
unrelated to any predator or herbivore population. The more we study 
communities, the more complexities we find, allowing ecologists to derive 
more accurate and sophisticated models of population dynamics. 


Herbivory describes the consumption of plants by insects and other animals, 
and it is another interspecific relationship that affects populations. Unlike 
animals, most plants cannot outrun predators or use mimicry to hide from 
hungry animals. Some plants have developed mechanisms to defend against 
herbivory. Other species have developed mutualistic relationships; for 
example, herbivory provides a mechanism of seed distribution that aids in 
plant reproduction. 


Defense Mechanisms against Predation and Herbivory 


The study of communities must consider evolutionary forces that act on the 
members of the various populations contained within it. Species are not 
static, but slowly changing and adapting to their environment by natural 
selection and other evolutionary forces. Species have evolved numerous 
mechanisms to escape predation and herbivory. These defenses may be 
mechanical, chemical, physical, or behavioral. 


Mechanical defenses, such as the presence of thorns on plants or the hard 
shell on turtles, discourage animal predation and herbivory by causing 
physical pain to the predator or by physically preventing the predator from 
being able to eat the prey. Chemical defenses are produced by many 
animals as well as plants, such as the foxglove which is extremely toxic 


when eaten. [link] shows some organisms’ defenses against predation and 


herbivory. 


(d) 


(c) 


The (a) honey locust tree (Gleditsia triacanthos) uses 
thorns, a mechanical defense, against herbivores, 
while the (b) Florida red-bellied turtle (Pseudemys 
nelsoni) uses its shell as a mechanical defense against 
predators. (c) Foxglove (Digitalis sp.) uses a chemical 
defense: toxins produced by the plant can cause 
nausea, vomiting, hallucinations, convulsions, or death 
when consumed. (d) The North American millipede 
(Narceus americanus) uses both mechanical and 
chemical defenses: when threatened, the millipede 
curls into a defensive ball and produces a noxious 
substance that irritates eyes and skin. (credit a: 
modification of work by Huw Williams; credit b: 


modification of work by “JamieS93”/Flickr; credit c: 
modification of work by Philip Jagenstedt; credit d: 
modification of work by Cory Zanker) 


Many species use their body shape and coloration to avoid being detected 
by predators. The crab spider has the coloration and body shape of a flower 
petal which makes it very hard to see when stationary against a background 
of real a real flower ([link]a). In another example, the chameleon can 
change its color to match its surroundings ([link]b). Both of these are 
examples of camouflage, or avoiding detection by blending in with the 
background. 


(a) The crab spider (a) and the chameleon (b) use 
body shape and/or coloration to deceive potential 
prey, and to prevent detection by predators. (credit a: 
photograph by David A. Rintoul; credit b: 
modification of work by Frank Vassen) 


Some species use coloration as a way of warning predators that they are not 
good to eat. For example, the cinnabar moth caterpillar, the fire-bellied 


toad, and many species of beetle have bright colors that warn of a foul taste, 
the presence of toxic chemical, and/or the ability to sting or bite, 
respectively. Predators that ignore this coloration and eat the organisms will 
experience their unpleasant taste or presence of toxic chemicals and learn 
not to eat them in the future. This type of defensive mechanism is called 
aposematic coloration, or warning coloration ((link]). 


St) 


(a) (b) 


(a) The strawberry poison dart frog (Oophaga 
pumilio) uses aposematic coloration to warn predators 
that it is toxic, while the (b) striped skunk (Mephitis 
mephitis) uses aposematic coloration to warn predators 
of the unpleasant odor it produces. (credit a: 
modification of work by Jay Iwasaki; credit b: 
modification of work by Dan Dzurisin) 


While some predators learn to avoid eating certain potential prey because of 
their coloration, other species have evolved mechanisms to mimic this 
coloration to avoid being eaten, even though they themselves may not be 
unpleasant to eat or contain toxic chemicals. In Batesian mimicry, a 
harmless species imitates the warning coloration of a harmful one. 
Assuming they share the same predators, this coloration then protects the 
harmless ones, even though they do not have the same level of physical or 
chemical defenses against predation as the organism they mimic. Many 
insect species mimic the coloration of wasps or bees, which are stinging, 
venomous insects, thereby discouraging predation ((link]). 


Batesian mimicry occurs when a harmless species 
mimics the coloration of a harmful species, as is seen 
with the (a) bumblebee and (b) bee-like robber fly. 
(credit a, b: modification of work by Cory Zanker) 


In Miillerian mimicry, multiple species share the same warning coloration, 
but all of them actually have defenses. [link] shows a variety of foul-tasting 
butterflies with similar coloration. 


Several unpleasant-tasting Heliconius 
butterfly species share a similar color 
pattern, an example of Miillerian mimicry. 
(credit: Joron M, Papa R, Beltran M, 
Chamberlain N, Mavarez J, et al.) 


Competition 


Resources are often limited within a habitat and multiple species may 
compete to obtain them. All species have an ecological niche in the 
ecosystem, which describes how they acquire the resources they need and 
how they interact with other species in the community. So, the plants in a 
garden are competing with each other for soil nutrients, and water. This 
competition between the different species is called interspecific 
competition. The overall effect on both species is negative because either 
one of the species would do better if the other species is not present. So, 
how do species reduce the overall negative effects of direct competition? 


Competitive Exclusion Principle 


The competitive exclusion principle states that two species cannot occupy 
the same niche in a habitat and stably coexist. In other words, different 
species cannot coexist in a community if they are competing for all the 
same resources. An example of this principle is shown in [link], with two 
protozoan species, Paramecium aurelia and Paramecium caudatum. When 
grown individually in the laboratory, they both thrive. But when they are 
placed together in the same test tube (habitat), P. aurelia outcompetes P. 
caudatum for food, leading to the latter’s eventual extinction. 


P. aurelia alone P. caudatum alone 


Number of cells 
rF FPN 


10 10 
Time (days) Time (days) 


Both species grown together 


NO N 
S isa} 
o oO 


ee 
an 


Number of cells 


10 
Time (days) 


Paramecium aurelia and Paramecium caudatum grow well 
individually, but when they compete for the same resources, 
the P. aurelia outcompetes the P. caudatum. 


Resource partitioning 

This exclusion may be avoided if a population evolves to make use of a 
different resource, a different area of the habitat, or feeds during a different 
time of day, called resource partitioning. The two organisms are then said to 
occupy different niches. These organisms coexist by minimizing direct 
competition. The anole lizards found on a single island are a good example 
of resource partitioning [link] because it shows the effects of how natural 
selection has driven the evolution of different species in order to reduce 
competition. 


; - incensis 


This figure shows resource partitioning among 11 
species of anole lizards found on the island of Puerto 
Rico. Each species occupies a different type or elevation 
of vegetation. The habitat is further partitioned by the 
amount of sunlight and moisture available. Image by Eva 
Horne modified from (Williams, E.E. 1983. Ecomorphs, 
faunas, island size, and diverse end points in island 
radiations of Anolis. In Lizard Ecology: Studies of a 


Model Organism. Eds. R.B. Huey, E.R. Pianka, and T.W. 
Schoener. Harvard University Press). 


Symbiosis 


Symbiotic relationships, or symbioses (plural), are close interactions 
between individuals of different species over an extended period of time 
that impact the abundance and distribution of the associating populations. 
Symbiosis is a greek word meaning “living together”. At least one of the 
species is dependent upon the other (they are not free-living), and often 
both species are dependent. Most scientists accept this definition, but some 
restrict the term to only those species that are mutualistic, where both 
individuals benefit from the interaction. In this discussion, the first broader 
definition will be used. 


Commensalism 


A commensal relationship occurs when one species benefits (+) from the 
close, prolonged interaction, while the other neither benefits nor is harmed 
(0). Birds nesting in trees provide an example of a commensal relationship 
({link]). The tree is not harmed by the presence of the nest among its 
branches. The nests are light and produce little strain on the structural 
integrity of the branch, and most of the leaves, which the tree uses to get 
energy by photosynthesis, are above the nest so they are unaffected. The 
bird, on the other hand, benefits greatly. If the bird had to nest in the open, 
its eggs and young would be vulnerable to predators. Another example of a 
commensal relationship is the clown fish and the sea anemone. The sea 
anemone is not harmed by the fish, and the fish gains protection from 
predators who would be stung upon nearing the sea anemone. 


The southern masked-weaver 
bird is starting to make a nest 
in a tree in Zambezi Valley, 
Zambia. This is an example 
of a commensal relationship, 
in which one species (the 
bird) benefits, while the other 
(the tree) neither benefits nor 
is harmed. (credit: 
“Hanay”/Wikimedia 
Commons) 


Mutualism 


A second type of species interaction is called mutualism, where two 
species benefit from their interaction (+,+). For example, termites have a 
mutualistic relationship with protozoa that live in the insect’s gut ([link]a). 
The termite benefits from the ability of bacterial symbionts within the 
protozoa to digest cellulose. The termite itself cannot do this, and without 
the protozoa, it would not be able to obtain energy from its food (cellulose 


from the wood it chews and eats). The protozoa and the bacterial symbionts 
benefit by having a protective environment and a constant supply of food 
from the wood chewing actions of the termite. Lichens have a mutualistic 
relationship between fungus and photosynthetic algae or bacteria ({link]b). 
As these symbionts grow together, the glucose produced by the algae 
provides nourishment for both organisms, whereas the physical structure of 
the lichen protects the algae from the elements and makes certain nutrients 
in the atmosphere more available to the algae. Another example of 
mutualism is the interaction between a plant and its insect pollinator. The 
plant benefits from having its pollen transferred to another individual to 
carry out reproduction and the insect benefits from nectar or other reward 
provided by the plant. This is an example of a non-symbiotic mutualism as 
both the plant and the insect are free-living organisms. 


(a) Termites form a mutualistic relationship with 
symbiotic protozoa in their guts, which allow both 
organisms to obtain energy from the cellulose the 
termite consumes. (b) Lichen is a fungus that has 
symbiotic photosynthetic algae living inside its cells. 
(credit a: modification of work by Scott Bauer, 
USDA; credit b: modification of work by Cory 
Zanker) 


Parasitism 


A parasite is an organism that lives in or on another living organism and 
derives nutrients from it. In this relationship, the parasite benefits (+), but 
the organism being fed upon, the host is harmed (-). The host is usually 
weakened by the parasite as it siphons resources the host would normally 
use to maintain itself. The parasite, however, is unlikely to kill the host, 
especially not quickly, because this would allow no time for the organism to 
complete its reproductive cycle by spreading to another host. 


The reproductive cycles of parasites are often very complex, sometimes 
requiring more than one host species. A tapeworm is a parasite that causes 
disease in humans when contaminated, undercooked meat such as pork, 
fish, or beef is consumed ([link]). The tapeworm can live inside the 
intestine of the host for several years, benefiting from the food the host is 
bringing into its gut by eating, and may grow to be over 50 ft long by 
adding segments. The parasite moves from species to species in a cycle, 
making two hosts necessary to complete its life cycle. Another common 
parasite is Plasmodium falciparum, the protozoan cause of malaria, a 
significant disease in many parts of the world. Living in human liver and 
red blood cells, the organism reproduces asexually in the gut of blood- 
feeding mosquitoes to complete its life cycle. Thus malaria is spread from 
human to human by mosquitoes, one of many arthropod-borne infectious 
diseases. 


Tapeworm (Taenia) Infection 


Embryos develop into 


larvae in muscles of Cysts may develop 
3) Tapeworm embryos pigs or humans. in any organ, and are most 
hatch, penetrate the common in subcutaneous 
intestinal wall, a A tissue as well as in the 
and circulate brain and eyes. 
to musculature 
in pigs or humans. Humans acquire the 
< infection by ingesting @} 


raw or undercooked 
meat from an infected 
animal host. 
O 
2 a/ 5) 
U The tapeworm 


2) Eggs or segments attaches itself 
are ingested by pigs to the intestine 
or humans. via hooks on 

the scolex. 


Eggs or tapeworm segments 
in feces are passed into 
the environment. 


Adults in small intestine 


This diagram shows the life cycle of a pork tapeworm (Taenia 
solium), a human worm parasite. (credit: modification of work 
by CDC) 


Amensalism 

Another type of interaction classified by biologists and ecologists is 
amensalism. Amensalism is any interaction between individuals of different 
species in which one individual is harmed (-) while the other individual is 
not affected (0). For example, as you walk down a side walk on a rainy day 
you step on an earthworm; the earthworm is negatively affected, and you 
are not affected. Amensalism occurs among micro-organisms when microbe 
species A releases chemicals that have a negative effect on microbe species 
B, but B has neither a positive nor negative effect on A. 


Coevolution 


When the genetic change in one species causes a subsequent change in the 
genetic structure of another species, this is called coevolution. In a 


community, all the interacting species have the potential to influence one 
another, and in a sense they are all evolving together. However, coevolution 
can only describe genetic changes in interacting species if scientists can 
demonstrate that specific interactions result in reciprocal adaptations. For 
example, a species of plant may rely solely on one species of insect for 
pollination and that one species of insect may only consume nectar from 
that one flower. Many of the above examples of species interactions do not 
fit the strict definition of coevolution, but one can not argue that these 
species are evolving in response to one another and their environment. 


Characteristics of Communities 


Communities are complex entities that can be characterized by their 
structure (the types and numbers of species present) and dynamics (how 
communities change over time). Understanding community structure and 
dynamics enables community ecologists to manage ecosystems more 
effectively. 


Foundation Species 


Foundation species are considered the “base” or “bedrock” of a community, 
having the greatest influence on its overall structure. They are usually the 
primary producers: organisms that bring most of the energy into the 
community. Kelp, brown algae, is a foundation species, forming the basis of 
the kelp forests off the coast of California. 


Foundation species may physically modify the environment to produce and 
maintain habitats that benefit the other organisms that use them. An 
example is the photosynthetic corals of the coral reef ({link]). Corals 
themselves are not photosynthetic, but harbor symbionts within their body 
tissues (dinoflagellates called zooxanthellae) that perform photosynthesis; 
this is another example of a mutualism. The exoskeletons of living and dead 
coral make up most of the reef structure, which protects many other species 
from waves and ocean currents. 


Coral is the foundation 
species of coral reef 
ecosystems. (credit: Jim E. 
Maragos, USFWS) 


Biodiversity, Species Richness, and Relative Species Abundance 


Biodiversity describes a community’s biological complexity: it is measured 
by the number of different species (species richness) in a particular area and 
their relative abundance (species evenness). The area in question could be a 
habitat, a biome, or the entire biosphere. Species richness is the term that is 
used to describe the number of species living in a habitat or biome. Species 
richness varies across the globe ({link]). One factor in determining species 
richness is latitude, with the greatest species richness occurring in 
ecosystems near the equator, which often have warmer temperatures, large 
amounts of rainfall, and low seasonality. The lowest species richness occurs 
near the poles, which are much colder, drier, and thus less conducive to life 
in Geologic time (time since glaciations). The predictability of climate or 
productivity is also an important factor. Other factors influence species 
richness as well. Relative species abundance is the number of individuals in 
a species relative to the total number of individuals in all species within a 
habitat, ecosystem, or biome. Foundation species often have the highest 
relative abundance of species. 


Number of mammal 
species per sq km 
Coo I 94-128 
({) 1-23 MM 129-154 
[Ej 24-42 GM 155-178 
3 43-60 Mi 179-228 
Gi 61-93 


The greatest species richness for 
mammals in North and South 
America is associated with the 

equatorial latitudes. (credit: 
modification of work by NASA, 
CIESIN, Columbia University) 


Keystone Species 


A keystone species is one species that has a disproportionately large effect 
on community structure relative to its biomass or abundance. The intertidal 
sea Star, Pisaster ochraceus, of the northwestern United States is a keystone 
species ({link]). Studies have shown that when this organism is removed 
from communities, populations of their natural prey (mussels) increase, 
completely altering the species composition and reducing biodiversity. 
Another keystone species is the banded tetra, a fish in tropical streams, 
which supplies nearly all of the phosphorus, a necessary inorganic nutrient, 
to the rest of the community. If these fish were to become extinct, the 
community would be greatly affected. 


The Pisaster ochraceus sea 
star is a keystone species. 
(credit: Jerry Kirkhart) 


Note: 

Everyday Connection 

Invasive Species 

Invasive species are non-native organisms that, when introduced to an area 
out of their native range, threaten the ecosystem balance of that habitat. 
Many such species exist in the United States, as shown in [link]. Whether 
enjoying a forest hike, taking a summer boat trip, or simply walking down 
an urban street, you have likely encountered an invasive species. 


4 
+ a a 
a re eo 


In the United States, invasive species like (a) purple 
loosestrife (Lythrum salicaria) and the (b) zebra mussel 
(Dreissena polymorpha) threaten certain aquatic 
ecosystems. Some forests are threatened by the spread of 
(c) common buckthorn (Rhamnus cathartica), (d) garlic 
mustard (Alliaria petiolata), and (e) the emerald ash borer 
(Agrilus planipennis). The (f) European starling (Sturnus 
vulgaris) may compete with native bird species for nest 
holes. (credit a: modification of work by Liz West; credit b: 
modification of work by M. McCormick, NOAA; credit c: 
modification of work by E. Dronkert; credit d: modification 
of work by Dan Davison; credit e: modification of work by 
USDA; credit f: modification of work by Don DeBold) 


One of the many recent proliferations of an invasive species concerns the 
growth of Asian carp populations. Asian carp were introduced to the 
United States in the 1970s by fisheries and sewage treatment facilities that 
used the fish’s excellent filter feeding capabilities to clean their ponds of 
excess plankton. Some of the fish escaped, however, and by the 1980s they 
had colonized many waterways of the Mississippi River basin, including 
the Illinois and Missouri Rivers. 


Voracious eaters and rapid reproducers, Asian carp may outcompete native 
species for food, potentially leading to their extinction. For example, black 
carp are voracious eaters of native mussels and snails, limiting this food 
source for native fish species. Silver carp eat plankton that native mussels 
and snails feed on, reducing this food source by a different alteration of the 
food web. In some areas of the Mississippi River, Asian carp species have 
become the most predominant, effectively outcompeting native fishes for 
habitat. In some parts of the Illinois River, Asian carp constitute 95 percent 
of the community's biomass. Although edible, the fish is bony and not a 
desired food in the United States. Moreover, their presence threatens the 
native fish and fisheries of the Great Lakes, which are important to local 
economies and recreational anglers. Asian carp have even injured humans. 
The fish, frightened by the sound of approaching motorboats, thrust 
themselves into the air, often landing in the boat or directly hitting the 
boaters. 

The Great Lakes and their prized salmon and lake trout fisheries are also 
being threatened by these invasive fish. Asian carp have already colonized 
rivers and canals that lead into Lake Michigan. One infested waterway of 
particular importance is the Chicago Sanitary and Ship Channel, the major 
supply waterway linking the Great Lakes to the Mississippi River. To 
prevent the Asian carp from leaving the canal, a series of electric barriers 
have been successfully used to discourage their migration; however, the 
threat is significant enough that several states and Canada have sued to 
have the Chicago channel permanently cut off from Lake Michigan. Local 
and national politicians have weighed in on how to solve the problem, but 
no one knows whether the Asian carp will ultimately be considered a 
nuisance, like other invasive species such as the water hyacinth and zebra 
mussel, or whether it will be the destroyer of the largest freshwater fishery 
of the world. 

The issues associated with Asian carp show how population and 
community ecology, fisheries management, and politics intersect on issues 
of vital importance to the human food supply and economy. Socio-political 
issues like this make extensive use of the sciences of population ecology 
(the study of members of a particular species occupying a particular area 
known as a habitat) and community ecology (the study of the interaction of 
all species within a habitat). 


Community Dynamics 


Community dynamics are the changes in community structure and 
composition over time. Sometimes these changes are induced by 
environmental disturbances such as volcanoes, earthquakes, storms, fires, 
and climate change. Communities with a stable structure are said to be at 
equilibrium. Following a disturbance, the community may or may not 
return to the equilibrium state. 


Succession describes the sequential appearance and disappearance of 
species in a community over time. In primary succession, newly exposed 
or newly formed land is colonized by living things; in secondary 
succession, part of an ecosystem is disturbed and remnants of the previous 
community remain. 


Primary Succession and Pioneer Species 


Primary succession occurs when new land is formed or rock is exposed: for 
example, following the eruption of volcanoes, such as those on the Big 
Island of Hawaii. As lava flows into the ocean, new land is continually 
being formed. On the Big Island, approximately 32 acres of land is added 
each year. First, weathering and other natural forces break down the 
substrate enough for the establishment of certain hearty plants and lichens 
with few soil requirements, known as pioneer species ((link]). These 
species help to further break down the mineral rich lava into soil where 
other, less hardy species will grow and eventually replace the pioneer 
species. In addition, as these early species grow and die, they add to an 
ever-growing layer of decomposing organic material and contribute to soil 
formation. Over time the area will reach an equilibrium state, with a set of 
organisms quite different from the pioneer species. 


During primary succession in 
lava on Maui, Hawaii, 
succulent plants are the 
pioneer species. (credit: 
Forest and Kim Starr) 


Secondary succession 


A classic example of secondary succession occurs in oak and hickory 
forests cleared by wildfire ([link]). Wildfires will burn most vegetation and 
kill those animals unable to flee the area. Their nutrients, however, are 
returned to the ground in the form of ash. Thus, even when areas are devoid 
of life due to severe fires, the area will soon be ready for new life to take 
hold. 


Before the fire, the vegetation was dominated by tall trees with access to the 
major plant energy resource: sunlight. Their height gave them access to 
sunlight while also shading the ground and other low-lying species. After 
the fire, though, these trees are no longer dominant. Thus, the first plants to 
grow back are usually annual plants followed within a few years by quickly 
growing and spreading grasses and other pioneer species. Due to, at least in 
part, changes in the environment brought on by the growth of the grasses 
and other species, over many years, shrubs will emerge along with small 
pine, oak, and hickory trees. These organisms are called intermediate 


species. Eventually, over 150 years, the forest will reach its equilibrium 
point where species composition is no longer changing and resembles the 
community before the fire. This equilibrium state is referred to as the 
climax community, which will remain stable until the next disturbance. 


Secondary Succession of an Oak and Hickory Forest 


Am 1 1 


a ~ : _ 2 Pelee he 
rien. ltl RIN 


Pioneer species Intermediate species Climax community 
Annual plants grow and are succeeded Shrubs, then pines, and young oak The mature oak and hickory forest 
by grasses and perennials. and hickory begin to grow. remains stable until the next disturbance. 


Secondary succession is shown in an oak and hickory forest 
after a forest fire. 


Ecosystem Experimentation and Modeling 


"Even if a scientific model, like a car, has only a few years to run before it 
is discarded, it serves its purpose for getting from one place to another." 
David L. Wingate, "Complex Clocks", Digestive Diseases and Sciences, 
1983, 28:1139 


Ecosystems are complex entities, with many components and variables, and 
thus they present quite a daunting task for ecosystem modelers. Life in an 
ecosystem is often about competition for limited resources, a characteristic 
of the mechanism of natural selection. Competition in communities (all 
living things within specific habitats) is observed both within species and 
among different species. The resources for which organisms compete 
include organic material from living or previously living organisms, 
sunlight, and mineral nutrients, which provide the energy for living 
processes and the matter to make up organisms’ physical structures. Other 
critical factors influencing community dynamics are the components of its 
physical and geographic environment: a habitat’s latitude, amount of 
rainfall, topography (elevation), and available species. These are all 
important environmental variables that determine which organisms can 
exist within a particular area. 


Furthermore, ecosystems are routinely exposed to various disturbances, or 
changes in the environment that effect their compositions: yearly variations 
in rainfall and temperature and the slower processes of plant growth, which 
may take several years. Many of these disturbances are a result of natural 
processes. For example, when lightning causes a forest fire and destroys 
part of a forest ecosystem, the ground is eventually populated by grasses, 
then by bushes and shrubs, and later by mature trees, restoring the forest to 
its former state. The impact of environmental disturbances caused by 
human activities is as important as the changes wrought by natural 
processes. Human agricultural practices, air pollution, acid rain, global 
deforestation, overfishing, eutrophication, oil spills, and illegal dumping on 
land and into the ocean are all issues of concern to conservationists. 


Research into Ecosystem Dynamics: Ecosystem 
Experimentation and Modeling 


The study of the changes in ecosystem structure caused by changes in the 
environment (disturbances) or by internal forces is called ecosystem 
dynamics. Ecosystems are characterized using a variety of research 
methodologies. Some ecologists study ecosystems using controlled 
experimental systems, while some study entire ecosystems in their natural 
state, and others use both approaches. 


A holistic ecosystem model attempts to quantify the composition, 
interaction, and dynamics of entire ecosystems; it is the most representative 
of the ecosystem in its natural state. A food web is an example of a holistic 
ecosystem model. However, this type of study is limited by time and 
expense, as well as the fact that it is neither feasible nor ethical to do 
experiments on large natural ecosystems. To quantify all different species in 
an ecosystem and the dynamics in their habitat is difficult, especially when 
studying large habitats such as the Amazon Rainforest, which covers 1.4 
billion acres (5.5 million km?) of the Earth’s surface. 


For these reasons, scientists study ecosystems under more controlled 
conditions. Experimental systems usually involve either partitioning a part 
of a natural ecosystem that can be used for experiments, termed a 
mesocosm, or by re-creating an ecosystem entirely in an indoor or outdoor 
laboratory environment, which is referred to as a microcosm. A major 
limitation to these approaches is that removing individual organisms from 
their natural ecosystem or altering a natural ecosystem through partitioning 
may change the dynamics of the ecosystem. These changes are often due to 
differences in species numbers and diversity and also to environment 
alterations caused by partitioning (mesocosm) or re-creating (microcosm) 
the natural habitat. Thus, these types of experiments are not totally 
predictive of changes that would occur in the ecosystem from which they 
were gathered. 


As both of these approaches have their limitations, some ecologists suggest 
that results from these experimental systems should be used only in 
conjunction with holistic ecosystem studies to obtain the most 
representative data about ecosystem structure, function, and dynamics. 


Scientists use the data generated by these experimental studies to develop 
ecosystem models that demonstrate the structure and dynamics of 


ecosystems. Three basic types of ecosystem modeling are routinely used in 
research and ecosystem management: a conceptual model, an analytical 
model, and a simulation model. A conceptual model is an ecosystem model 
that consists of flow charts to show interactions of different compartments 
of the living and nonliving components of the ecosystem. A conceptual 
model describes ecosystem structure and dynamics and shows how 
environmental disturbances affect the ecosystem; however, its ability to 
predict the effects of these disturbances is limited. Analytical and 
simulation models, in contrast, are mathematical methods of describing 
ecosystems that are indeed capable of predicting the effects of potential 
environmental changes without direct experimentation, although with some 
limitations as to accuracy. An analytical model is an ecosystem model that 
is created using simple mathematical formulas to predict the effects of 
environmental disturbances on ecosystem structure and dynamics. A 
simulation model is an ecosystem model that is created using complex 
computer algorithms to holistically model ecosystems and to predict the 
effects of environmental disturbances on ecosystem structure and dynamics. 
Ideally, these models are accurate enough to determine which components 
of the ecosystem are particularly sensitive to disturbances, and they can 
Serve as a guide to ecosystem managers (such as conservation ecologists or 
fisheries biologists) in the practical maintenance of ecosystem health. 


Conceptual Models 


Conceptual models are useful for describing ecosystem structure and 
dynamics and for demonstrating the relationships between different 
organisms in a community and their environment. Conceptual models are 
usually depicted graphically as flow charts. The organisms and their 
resources are grouped into specific compartments with arrows showing the 
relationship and transfer of energy or nutrients between them. 


To model the cycling of mineral nutrients, organic and inorganic nutrients 
are subdivided into those that are bioavailable (ready to be incorporated into 
biological macromolecules) and those that are not. For example, in a 
terrestrial ecosystem near a deposit of coal, carbon will be available to the 
plants of this ecosystem as carbon dioxide gas in a short-term period, not 


from the carbon-rich coal itself. However, over a longer period, 
microorganisms capable of digesting coal will incorporate its carbon or 
release it as natural gas (methane, CH,), changing this unavailable organic 
source into an available one. This conversion is greatly accelerated by the 
combustion of fossil fuels by humans, which releases large amounts of 
carbon dioxide into the atmosphere. This is thought to be a major factor in 
the rise of the atmospheric carbon dioxide levels in the industrial age. The 
carbon dioxide released from burning fossil fuels is produced faster than 
photosynthetic organisms can use it. This process is intensified by the 
reduction of photosynthetic trees because of worldwide deforestation. Most 
scientists agree that high atmospheric carbon dioxide is a major cause of 
global climate change. 


Analytical and Simulation Models 


The major limitation of conceptual models is their inability to predict the 
consequences of changes in ecosystem species and/or environment. 
Ecosystems are dynamic entities and subject to a variety of abiotic and 
biotic disturbances caused by natural forces and/or human activity. 
Ecosystems altered from their initial equilibrium state can often recover 
from such disturbances and return to a state of equilibrium. As most 
ecosystems are subject to periodic disturbances and are often in a state of 
change, they are usually either moving toward or away from their 
equilibrium state. There are many of these equilibrium states among the 
various components of an ecosystem, which affects the ecosystem overall. 
Furthermore, as humans have the ability to greatly and rapidly alter the 
species content and habitat of an ecosystem, the need for predictive models 
that enable understanding of how ecosystems respond to these changes 
becomes more crucial. 


Analytical models often use simple, linear components of ecosystems, such 
as food chains, and are known to be complex mathematically; therefore, 
they require a significant amount of mathematical knowledge and expertise. 
Although analytical models have great potential, their simplification of 
complex ecosystems is thought to limit their accuracy. Simulation models 


that use computer programs are better able to deal with the complexities of 
ecosystem structure. 


A recent development in simulation modeling uses supercomputers to 
create and run individual-based simulations, which accounts for the 
behavior of individual organisms and their effects on the ecosystem as a 
whole. These simulations are considered to be the most accurate and 
predictive of the complex responses of ecosystems to disturbances. 


Nitrogen and Phosphorus Cycles 


"As mouths multiply, food resources dwindle. Land is a limited quantity, 
and the land that will grow wheat is absolutely dependent on difficult and 
capricious natural phenomena... I have to point the way out of this colossal 
dilemma. It is the chemist who must come to the rescue of the threatened 
communities. It is through the laboratory that starvation may ultimately be 
turned into plenty... The fixation of atmospheric nitrogen is one of the great 
discoveries, awaiting the genius of chemists." William Crookes, Chemical 
News. 1898, 78:125. 


The "difficult and capricious natural phenomena" of nitrogen fixation is just 
one part of the biogeochemical cycle of this nutrient, but it is, as Crookes 
noted, an extremely important part. Chemists have succeeded in the quest to 
develop reactions that can fix atmospheric nitrogen into forms that can be 
used by living organisms, but it should be noted that humble 
microorganisms did this long before boastful chemists thought about it. 
Industrial processes for nitrogen fixation now produce as much usable 
nitrogen as all of the biological nitrogen-fixers on the planet. This chemical 
success, however, does come with some undesirable consequences, as you 
will learn below. 


Energy flows directionally through ecosystems, entering as sunlight (or 
inorganic molecules for chemoautotrophs) and leaving as heat during the 
many transfers between trophic levels. However, the matter that makes up 
living organisms is conserved and recycled. The six most common elements 
associated with organic molecules—carbon, nitrogen, hydrogen, oxygen, 
phosphorus, and sulfur—take a variety of chemical forms and may exist for 
long periods in the atmosphere, on land, in water, or beneath the Earth’s 
surface. Geologic processes, such as weathering, erosion, water drainage, 
and the subduction of the continental plates, all play a role in this recycling 
of materials. Because geology and chemistry have major roles in the study 
of this process, the recycling of inorganic matter between living organisms 
and their environment is called a biogeochemical cycle. 


The Nitrogen Cycle 


Nitrogen is an essential nutrient for living processes; it is a major 
component of proteins and nucleic acids. Proteins are important biological 
molecules because all cellular activities are driven by proteins. Nucleic 
acids are the building blocks of DNA (hereditary material). Nitrogen is 
often the limiting nutrient (necessary for growth) on terrestrial ecosystems 
[link]. 


Getting nitrogen into the living world is difficult. Plants and phytoplankton 
are not equipped to incorporate nitrogen from the atmosphere (which exists 
as tightly bonded, triple covalent N>) even though this molecule comprises 
approximately 78 percent of the atmosphere. Nitrogen enters the living 
world via free-living and symbiotic bacteria, which incorporate nitrogen 
into their macromolecules through nitrogen fixation (conversion of N>). 
Cyanobacteria live in most aquatic ecosystems where sunlight is present; 
they play a key role in nitrogen fixation. Cyanobacteria are able to use 
inorganic sources of nitrogen to “fix” nitrogen. Rhizobium bacteria live 
symbiotically in the root nodules of legumes (such as peas, beans, and 
peanuts) and provide them with the organic nitrogen they need. Free-living 
bacteria, such as Azotobacter, are also important nitrogen fixers. In addition 
to natural nitrogen fixation by microbes, humans industrially fix nitrogen to 
produce artificial fertilizers. 


Organic nitrogen is especially important to the study of ecosystem 
dynamics since many ecosystem processes, such as primary production and 
decomposition, are limited by the available supply of nitrogen. As shown in 
[link], the nitrogen that enters living systems by nitrogen fixation is 
successively converted from organic nitrogen back into nitrogen gas by 
bacteria. This process occurs in three steps in terrestrial systems: 
ammonification, nitrification, and denitrification. First, the ammonification 
process converts nitrogenous waste from living animals or from the remains 
of dead animals into ammonium (NH,") by certain bacteria and fungi. 
Second, the ammonium is converted to nitrites (NO> _) by nitrifying 
bacteria, such as Nitrosomonas, through nitrification. Subsequently, nitrites 
are converted to nitrates (NO3_) by similar organisms. Third, the process of 
denitrification occurs, whereby bacteria, such as Pseudomonas and 
Clostridium, convert the nitrates into nitrogen gas, allowing it to re-enter 
the atmosphere. 


The Whit EhyCyvele 


Denitrification 
by bacteria 
/\ 
fm 
| 
J 
Nitrification by Nitrogenous 
bacteria to NO; wastes in soil 


V 
- ee Ammonification Nitrogen 

Nitrification by «4 _____ by bacteria and << fixation 

bacteria to NOZ > fungi to NH,* S ~ by bacteria 


Nitrogen enters the living world from the atmosphere via 
nitrogen-fixing bacteria. This nitrogen and nitrogenous waste 
from animals is then processed back into gaseous nitrogen by 
soil bacteria, which also supply terrestrial food webs with the 

organic nitrogen they need. (credit: modification of work by 
John M. Evans and Howard Perlman, USGS) 


Human activity can release nitrogen into the environment by two primary 
means: the combustion of fossil fuels, which releases different nitrogen 
oxides, and by the use of artificial fertilizers in agriculture, which are then 
washed into lakes, streams, and rivers by surface runoff. Atmospheric 
nitrogen is associated with several effects on Earth’s ecosystems including 
the production of acid rain (as nitric acid, HNO3) and greenhouse gas (as 
nitrous oxide, N»O) potentially causing climate change. A major effect from 
fertilizer runoff is saltwater and freshwater eutrophication, a process 
whereby nutrient runoff causes the excess growth of microorganisms, 
depleting dissolved oxygen levels and killing ecosystem fauna. 


A similar process occurs in the marine nitrogen cycle, where the 
ammonification, nitrification, and denitrification processes are performed 
by marine bacteria. Some of this nitrogen falls to the ocean floor as 
sediment, which can then be moved to land in geologic time by uplift of the 
Earth’s surface and thereby incorporated into terrestrial rock. Although the 
movement of nitrogen from rock directly into living systems has been 
traditionally seen as insignificant compared with nitrogen fixed from the 
atmosphere, a recent study showed that this process may indeed be 
significant and should be included in any study of the global nitrogen cycle. 
[footnote] 

Scott L. Morford, Benjamin Z. Houlton, and Randy A. Dahlgren, 
“Increased Forest Ecosystem Carbon and Nitrogen Storage from Nitrogen 
Rich Bedrock,” Nature 477, no. 7362 (2011): 78-81. 


The Phosphorus Cycle 


Phosphorus is another essential nutrient for living processes; it is a major 
component of nucleic acids, phospholipids, and, as calcium phosphate, 
makes up the supportive components of our bones. Phosphorus is often the 
limiting nutrient (necessary for growth) in aquatic ecosystems ([link]). 


Phosphorus occurs in nature as the phosphate ion (PO,° ). In addition to 
phosphate runoff as a result of human activity (mined to make artificial 
fertilizers), natural surface runoff occurs when it is leached from phosphate- 
containing rock by weathering, thus sending phosphates into rivers, lakes, 
and the ocean. This rock has its origins in the ocean. Phosphate-containing 
ocean sediments form primarily from the bodies of ocean organisms and 
from their excretions. However, in remote regions, volcanic ash, aerosols, 
and mineral dust may also be significant phosphate sources. This sediment 
then is moved to land over geologic time by the uplifting of areas of the 
Earth’s surface. 


Phosphorus is also reciprocally exchanged between phosphate dissolved in 
the ocean and marine ecosystems. The movement of phosphate from the 
ocean to the land and through the soil is extremely slow, with the average 
phosphate ion having an oceanic residence time between 20,000 and 
100,000 years. 


In nature, phosphorus exists as the phosphate ion (PO,° ). 
Weathering of rocks and volcanic activity releases phosphate 
into the soil, water, and air, where it becomes available to 
terrestrial food webs. Phosphate enters the oceans via surface 
runoff, groundwater flow, and river flow. Phosphate dissolved 
in ocean water cycles into marine food webs. Some phosphate 
from the marine food webs falls to the ocean floor, where it 
forms sediment. (credit: modification of work by John M. 
Evans and Howard Perlman, USGS) 


Excess phosphorus and nitrogen that enters these ecosystems from fertilizer 
runoff and from sewage causes excessive growth of microorganisms and 
depletes the dissolved oxygen, which leads to the death of many ecosystem 
fauna, such as shellfish and finfish. This process is responsible for dead 
zones in lakes and at the mouths of many major rivers ([link]). 


Particulate Organic Carbon (mg/m') Population Density (persons/km’) Dead Zone Size (km’) 


unkown « . + 
10 20 $0 100 ©6200 $00 1,000 ! 10 100 1,000 10k 100k 0.1 + 10 100 Ik 10k 


Dead zones occur when phosphorus and nitrogen from 
fertilizers cause excessive growth of microorganisms, which 
depletes oxygen and kills fauna. Worldwide, large dead zones 
are found in coastal areas of high population density. (credit: 
NASA Earth Observatory) 


A dead zone is an area within a freshwater or marine ecosystem where 
large areas are depleted of their normal flora and fauna; these zones can be 
caused by eutrophication, oil spills, dumping of toxic chemicals, and other 
human activities. The number of dead zones has been increasing for several 
years, and more than 400 of these zones were present as of 2008. One of the 
worst dead zones is off the coast of the United States in the Gulf of Mexico, 
where fertilizer runoff from the Mississippi River basin has created a dead 
zone of over 8463 square miles. Phosphate and nitrate runoff from 
fertilizers also negatively affect several lake and bay ecosystems including 
the Chesapeake Bay in the eastern United States. 


Note: 


Everyday Connection 
Chesapeake Bay 


(a) 


This (a) satellite image shows 
the Chesapeake Bay, an 
ecosystem affected by 
phosphate and nitrate runoff. A 
(b) member of the Army Corps 
of Engineers holds a clump of 
oysters being used as a part of 
the oyster restoration effort in 
the bay. (credit a: modification 
of work by NASA/MODIS; 
credit b: modification of work 
by U.S. Army) 


The Chesapeake Bay has long been valued as one of the most scenic areas 
on Earth; it is now in distress and is recognized as a declining ecosystem. 
In the 1970s, the Chesapeake Bay was one of the first ecosystems to have 
identified dead zones, which continue to kill many fish and bottom- 
dwelling species, such as clams, oysters, and worms. Several species have 
declined in the Chesapeake Bay due to surface water runoff containing 
excess nutrients from artificial fertilizer used on land. The source of the 
fertilizers (with high nitrogen and phosphate content) is not limited to 


agricultural practices. There are many nearby urban areas and more than 
150 rivers and streams empty into the bay that are carrying fertilizer runoff 
from lawns and gardens. Thus, the decline of the Chesapeake Bay is a 
complex issue and requires the cooperation of industry, agriculture, and 
everyday homeowners. 

Of particular interest to conservationists is the oyster population; it is 
estimated that more than 200,000 acres of oyster reefs existed in the bay in 
the 1700s, but that number has now declined to only 36,000 acres. Oyster 
harvesting was once a major industry for Chesapeake Bay, but it declined 
88 percent between 1982 and 2007. This decline was due not only to 
fertilizer runoff and dead zones but also to overharvesting. Oysters require 
a certain minimum population density because they must be in close 
proximity to reproduce. Human activity has altered the oyster population 
and locations, greatly disrupting the ecosystem. 

The restoration of the oyster population in the Chesapeake Bay has been 
ongoing for several years with mixed success. Not only do many people 
find oysters good to eat, but they also clean up the bay. Oysters are filter 
feeders, and as they eat, they clean the water around them. In the 1700s, it 
was estimated that it took only a few days for the oyster population to filter 
the entire volume of the bay. Today, with changed water conditions, it is 
estimated that the present population would take nearly a year to do the 
same job. 

Restoration efforts have been ongoing for several years by non-profit 
organizations, such as the Chesapeake Bay Foundation. The restoration 
goal is to find a way to increase population density so the oysters can 
reproduce more efficiently. Many disease-resistant varieties (developed at 
the Virginia Institute of Marine Science for the College of William and 
Mary) are now available and have been used in the construction of 
experimental oyster reefs. Efforts to clean and restore the bay by Virginia 
and Delaware have been hampered because much of the pollution entering 
the bay comes from other states, which stresses the need for inter-state 
cooperation to gain successful restoration. 

The new, hearty oyster strains have also spawned a new and economically 
viable industry—oyster aquaculture—which not only supplies oysters for 
food and profit, but also has the added benefit of cleaning the bay. 


Freshwater Biomes 


Introduction 

"For as the element of water lies in the middle of the globe, so, the branches 
run out from the root in its circuit on all sides towards the plains and 
towards the light. From this root very many branches are born." Paracelsus, 
"The Philosophy of the Generation of the Elements", Book the Fourth, Text 
II. In The Hermetic and Alchemical Writings of Aureolus Phillipus 
Theophrastus Bombast, of Hohenheim, called Paracelsus the Great, 
translated by A.E. Waite (1894), 1:232. 


The alchemical thinking of Paracelsus might seem unscientific today, but 
his insights about the central nature of water are still viable. Freshwater 
biomes are among the most important on the planet in terms of species 
diversity and ecosystem services. Abiotic and biotic (including human) 
impacts on these biomes are among the most important factors in 
influencing these functions, and their role in the various biogeochemical 
cycles cannot be overstated. 


Abiotic Factors Influencing Aquatic Biomes 


Aquatic biomes are influenced by a series of abiotic factors associated with 
water, and these factors include the amount of light, stratification due to 
temperature, and the thermal properties of water. Another abiotic factor is 
nutrients, review the following information about freshwater biomes and 
begin to think about how human disturbances can affect freshwater 
ecosystems. 


Freshwater Biomes 


Freshwater biomes include lakes and ponds (standing water) as well as 
rivers and streams (flowing water). They also include wetlands, which will 
be discussed later. Humans rely on freshwater biomes to provide aquatic 
resources for drinking water, crop irrigation, sanitation, and industry. These 
various roles and human benefits are referred to as ecosystem services. 
Lakes and ponds are found in terrestrial landscapes and are, therefore, 


connected with abiotic and biotic factors influencing these terrestrial 
biomes. 


Lakes and Ponds 


Lakes and ponds can range in area from a few square meters to thousands 
of square kilometers. Temperature is an important abiotic factor affecting 
living things found in lakes and ponds. In the summer, thermal stratification 
of lakes and ponds occurs when the upper layer of water is warmed by the 
sun and does not mix with deeper, cooler water. Light can penetrate within 
the photic zone of the lake or pond. Phytoplankton (algae and 
cyanobacteria) are found here and carry out photosynthesis, providing the 
base of the food web of lakes and ponds. Zooplankton, such as rotifers and 
small crustaceans, consume these phytoplankton. At the bottom of lakes 
and ponds, bacteria in the aphotic zone break down dead organisms that 
sink to the bottom. 


Nitrogen and phosphorus are important limiting nutrients in lakes and 
ponds. Because of this, they are determining factors in the amount of 
phytoplankton growth in lakes and ponds. When there is a large input of 
nitrogen and phosphorus (from sewage and runoff from fertilized lawns and 
farms, for example), the growth of algae skyrockets, resulting in a large 
accumulation of algae called an algal bloom. Algal blooms can become so 
extensive that they reduce light penetration in water. As a result, the lake or 
pond becomes aphotic and photosynthetic plants cannot survive. When the 
algae die and decompose, severe oxygen depletion of the water occurs. 
Fishes and other organisms that require oxygen are then more likely to die, 
and resulting dead zones are found across the globe. Lake Erie and the Gulf 
of Mexico represent freshwater and marine habitats where phosphorus 
control and storm water runoff pose significant environmental challenges. 


Rivers and Streams 


Rivers and streams are continuously moving bodies of water that carry large 
amounts of water from the source, or headwater, to a lake or ocean. The 
largest rivers include the Nile River in Africa, the Amazon River in South 
America, and the Mississippi River in North America. 


Abiotic features of rivers and streams vary along the length of the river or 
stream. Streams begin at a point of origin referred to as source water. The 
source water is usually cold, low in nutrients, and clear. The channel (the 
width of the river or stream) is narrower than at any other place along the 
length of the river or stream. Because of this, the current is often faster here 
than at any other point of the river or stream. 


The fast-moving water results in minimal silt accumulation at the bottom of 
the river or stream; therefore, the water is clear. Photosynthesis here is 
mostly attributed to algae that are growing on rocks; the swift current 
inhibits the growth of phytoplankton. An additional input of energy can 
come from leaves or other organic material that falls into the river or stream 
from trees and other plants that border the water. When the leaves 
decompose, the organic material and nutrients in the leaves are returned to 
the water. Plants and animals have adapted to this fast-moving water. For 
instance, leeches (phylum Annelida) have elongated bodies and suckers on 
both ends. These suckers attach to the substrate, keeping the leech anchored 
in place. Freshwater trout species (phylum Chordata) are an important 
predator in these fast-moving rivers and streams. 


As the river or stream flows away from the source, the width of the channel 
gradually widens and the current slows. This slow-moving water, caused by 
the gradient decrease and the volume increase as tributaries unite, has more 
sedimentation. Phytoplankton can also be suspended in slow-moving water. 
Therefore, the water will not be as clear as it is near the source. The water is 
also warmer. Worms (phylum Annelida) and insects (phylum Arthropoda) 
can be found burrowing into the mud. The higher order predator vertebrates 
(phylum Chordata) include waterfowl, frogs, and fishes. These predators 
must find food in these slow moving, sometimes murky, waters and, unlike 
the trout in the waters at the source, these vertebrates may not be able to use 
vision as their primary sense to find food. Instead, they are more likely to 
use taste or chemical cues to find prey. 


Wetlands 


Wetlands are environments in which the soil is either permanently or 
periodically saturated with water. Wetlands are different from lakes because 
wetlands are shallow bodies of water whereas lakes vary in depth. Emergent 
vegetation consists of wetland plants that are rooted in the soil but have 
portions of leaves, stems, and flowers extending above the water’s surface. 
There are several types of wetlands including marshes, swamps, bogs, 
mudflats, and salt marshes. The three shared characteristics among these 
types—what makes them wetlands—are their hydrology, hydrophytic 
vegetation, and hydric soils. 


Freshwater marshes and swamps are characterized by slow and steady 
water flow. Bogs develop in depressions where water flow is low or 
nonexistent. Bogs usually occur in areas where there is a clay bottom with 
poor percolation. Percolation is the movement of water through the pores in 
the soil or rocks. The water found in a bog is stagnant and oxygen depleted 
because the oxygen that is used during the decomposition of organic matter 
is not replaced. As the oxygen in the water is depleted, decomposition 
slows. This leads to organic acids and other acids building up and lowering 
the pH of the water. At a lower pH, nitrogen becomes unavailable to plants. 
This creates a challenge for plants because nitrogen is an important limiting 
resource. Some types of bog plants (such as sundews, pitcher plants, and 
Venus flytraps) capture insects and extract the nitrogen from their bodies. 
Bogs have low net primary productivity because the water found in bogs 
has low levels of nitrogen and oxygen. 


Population Growth Curves 


Introduction 

"Population, when unchecked, increases in a geometrical ratio. Subsistence 
increases only in an arithmetical ratio. A slight acquaintance with numbers 
will show the immensity of the first power in comparison with the second." 
Thomas Malthus, An Essay on the Principle of Populations, 1798 


Malthus recognized the fact that there is a connection between resources 
and population growth, and that one of these (population growth) can 
increase at a greater rate than the other. Modern population ecologists make 
use of a variety of methods to model population dynamics mathematically. 
These more precise models can then be used to accurately describe changes 
occurring in a population and better predict future changes. Use the 
following information to make sure that you have at least a "slight 
acquaintance" with the mathematical principles that are used to describe 
population growth. 


Exponential Growth 


Charles Darwin, in his theory of natural selection, was greatly influenced by 
the English clergyman Thomas Malthus. Malthus published a book in 1798 
stating that populations with unlimited natural resources grow very rapidly. 
This accelerating pattern of increasing population size is called exponential 
growth. 


The best example of exponential growth is seen in bacteria. Some species of 
Bacteria can undergo cell division about every hour. If 1000 bacteria are 
placed in a large flask with an unlimited supply of nutrients (so the nutrients 
will not become depleted), after an hour, there is one round of division and 
each organism divides, resulting in 2000 organisms—an increase of 1000. 
In another hour, each of the 2000 organisms will double, producing 4000, 
an increase of 2000 organisms. After the third hour, there should be 8000 
bacteria in the flask, an increase of 4000 organisms. The important concept 
of exponential growth is that the population growth rate—the number of 
organisms added in each reproductive generation—is accelerating; that is, it 
is increasing at a greater and greater rate. After 1 day and 24 of these 


cycles, the population would have increased from 1000 to more than 16 
billion. When the population size, N, is plotted over time, a J-shaped 
growth curve is produced ([link]). 


Exponential growth is common when population organisms have unlimited 
resources. The growth of that population can be calculated using the 
equation below. For further explanation of this equation please go to 
Population Growth . 

Equation: 


G=rN 


The value "r” can be positive, meaning the population is increasing in size; 
or negative, meaning the population is decreasing in size; or zero, where the 
population’s size is unchanging, a condition known as zero population 
growth. A further refinement of the formula recognizes that different 
species have inherent differences in their per capita growth rates (r), even 
under ideal conditions. Obviously, a bacterium can reproduce more rapidly 
and have a higher per capita growth rate than a human. The maximal 
growth rate for a species is its biotic potential, or r,,,,, thus changing the 
equation to: 

Equation: 


G = TmaxN 


© co) 
N N 
n wn 
i= c 
2 iS] 
& & 
S = 
a a 
{o) [o) 
a a 


When resources are unlimited, populations exhibit 
exponential growth, resulting in a J-shaped curve. 
When resources are limited, populations exhibit 
logistic growth. In logistic growth, population 
expansion decreases as resources become scarce, and 
it levels off when the carrying capacity of the 
environment is reached, resulting in an S-shaped 
curve. 


Logistic Growth 


Exponential growth is possible only when infinite natural resources are 
available; this is not the case in the real world. Charles Darwin recognized 
this fact in his description of the “struggle for existence,” which states that 
individuals will compete (with members of their own or other species) for 
limited resources. The successful ones will survive to pass on their own 
characteristics and traits (which we know now are transferred by genes) to 
the next generation at a greater rate (natural selection). To model the reality 
of limited resources, population ecologists developed the logistic growth 
model. 


Carrying Capacity and the Logistic Model 


In the real world, with its limited resources, exponential growth cannot 
continue indefinitely. Exponential growth may occur in environments where 
there are few individuals and plentiful resources, but when the number of 
individuals gets large enough, resources will be depleted, slowing the 
growth rate. Eventually, the growth rate will plateau or level off ((link]). 
This population size, which represents the maximum population size that a 
particular environment can support, is called the carrying capacity, or K. 


The formula we use to calculate logistic growth adds the carrying capacity 
as a moderating force in the growth rate. The expression “K — N” is 


indicative of how many individuals may be added to a population at a given 
stage, and “K — N” divided by “K” is the fraction of the carrying capacity 
available for further growth. Thus, the exponential growth model is 
restricted by this factor to generate the logistic growth equation: 

Equation: 


(K — N) 


G =TmaxlV 7 


Notice that when N is very small, (K-N)/K becomes close to K/K or 1, and 
the right side of the equation reduces to rj4,V, which means the population 
is growing exponentially and is not influenced by carrying capacity. On the 
other hand, when N is large, (K-N)/K come close to zero, which means that 
population growth will be slowed greatly or even stopped. Thus, population 
growth is greatly slowed in large populations by the carrying capacity K. 
This model also allows for the population of a negative population growth, 
or a population decline. This occurs when the number of individuals in the 
population exceeds the carrying capacity (because the value of (K-N)/K is 
negative). 


A graph of this equation yields an S-shaped curve ({link]), and it is a more 
realistic model of population growth than exponential growth. There are 
three different sections to an S-shaped curve. Initially, growth is exponential 
because there are few individuals and ample resources available. Then, as 
resources begin to become limited, the growth rate decreases. Finally, 
growth levels off at the carrying capacity of the environment, with little 
change in population size over time. 


Introduction to Water Pollution 


The Water Pollution Crisis 
Introduction 


Pollution, pollution, 
You can use the latest toothpaste, 
And then rinse your mouth with industrial waste. 


Tom Lehrer, lyrics from his 1965 song Pollution 


The effects humans have on the water cycle and fresh water supply 
described one aspect of the global water crisis, specifically the water 
shortages that afflict many arid and densely populated areas. The global 
water crisis also involves water pollution, because to be useful for drinking 
and irrigation, water must not be polluted beyond certain thresholds. 
According to the World Health Organization, in 2008 approximately 880 
million people in the world (or 13% of world population) did not have 
access to improved (safe) drinking water (World Health Statistics, 2010) 
({link]). At the same time, about 2.6 billion people (or 40% of world 
population) lived without improved sanitation ([link]), which is defined as 
having access to a public sewage system, septic tank, or even a simple pit 
latrine. Each year approximately 1.7 million people die from diarrheal 
diseases associated with unsafe drinking water, inadequate sanitation, and 
poor hygiene, e.g., hand washing with soap. Almost all of these deaths are 
in developing countries, and around 90% of them occur among children 
under the age of 5 (see Figure [link]). Compounding the water crisis is the 
issue of social justice; poor people more commonly lack clean water and 
Sanitation than wealthy people in similar areas. Globally, improving water, 
sanitation, and hygiene could prevent up to 9% of all disease and 6% of all 
deaths. In addition to the global waterborne disease crisis, chemical 
pollution from agriculture, industry, cities, and mining threatens global 
water quality. Some chemical pollutants have serious and well-known 
health effects; however, many others have poorly known long-term health 
effects. In the U.S. currently more than 40,000 water bodies fit the 
definition of “impaired” set by EPA (See Figure [link]), which means they 


could neither support a healthy ecosystem nor meet water quality standards. 
In Gallup public polls conducted over the past decade Americans 
consistently put water pollution and water supply as the top environmental 
concerns over issues such as air pollution, deforestation, species extinction, 
and global warming. 


Tihok ezaatectaet itd mre Petes tl ad ca rca aed i Ob ge ec age era a reg pare at LC (Date Sauce raid Meal Depancaten World Healt 
ea ak pat ao the Bord Pina Cogan care eorany het lage wate of gay courier teary, by aaa ar ol Bn decent, ‘Mig Prchectare: Pubs Haut litlaomaian igaitege 
ap crneerng fhe deidaber ih borden ca bourdlaraa figded fae on mug reprenerd eppeecrrata bev der Nea fer ahah med Gagne Ind oeabors bysberea $05) Organi 
hare ray rol pel eka eee feed HEM Organcite OYE 0) A ight eae 


Proportion of Population by Country Using Improved Drinking 
Water Sources in 2008 Improved drinking water sources, e.g., 
household connections, public standpipes, boreholes, protected dug 
wells and springs, and rainwater collections, are defined as those more 
likely to provide safe water than unimproved water sources, e.g., 
unprotected wells and springs, vendor-provided water, bottled water 
(unless water for other uses is available from an improved source), and 
tanker truck-provided water. Source: World Health Organization 


Tha echt nl aed CMa a Hd arp kil 8, ink, uh ily Med ais hy Ei sD abt Tht emai: Wankel Pei pana tons Weed Health 
ta peut od hae ilaid (Hepa Cerpamcy ation coaching ek legal ial ae aarp timate Aare iy Ra a ce Mlag: Predict, Paatde: Heaths bisarraiten inalign 
Dreemevreang Be deleadabon of dy beedart or Burda Cosel bray ce reap regener apeseermagds Beedle Dear bon a wed peg phe before Sydeen (LES, Orga . 

fare muy col pod ise Hall agree, Vietd Hag Cegancaten GWHO-DYH Milage ' 


Proportion of Population by Country Using Improved Sanitation 
Facilities in 2008 Improved sanitation facilities, e.g., connection to 
public sewers or septic systems, pour-flush latrines, pit latrines, and 

ventilated improved pit latrines, are defined as those more likely to be 

sanitary than unimproved facilities, e.g., bucket latrines, public 
latrines, and open pit latrines. Source: World Health Organization 


of 


Deaths per 100000 children 
|__]o=100 

[) 101-200 

a si-0 

a ci 

He + 

[| Data not avaitabte 

[7] Nict appticatile 


‘That bebaretharar. rel ramet. betawt ated hon cbesagranpe wel det Ghat aps de terres Pan ede ericens fol erty operat wheal carved Chats Sheraton, bed Manali Dirgearaziateh " ‘World Health 
on Bbw pad of the World laa Gegarataton concerreng the legal viatun of any country, bemiory, off of aren ot of oo tore, Allap Procectore Putte Hawt infcrsaiion Organization 
a cmaning he deiméaton of 6 berber a bsurdanen Deded bras on mapa regreeet appa areata beceder Beau ter afachs and Gecgrapte: lefiomrution ‘Syutena (LETS) : 

Waka ty ah et ok ll ge eve ‘eget al Spear apt, HO S00) Allnghh erred 


Deaths by Country from Diarrhea Caused by Unsafe Water, 
Unimproved Sanitation, and Poor Hygiene in Children Less than 5 
Years Old, 2004 Source: World Health Organization 


Impaired 9“ 
Waters-1998 R 
(Updated Feb. 2000) 


No Waters Listed 
me <5% 
Ge 5 - 10% 
We 10-25% 
Ma > 25% 


Percentage of Impaired Water Bodies in a Watershed by State 
in USA Based on US EPA Data in 2000 Map of watersheds 
containing impaired water bodies from the U.S. Environmental 
Protection Agency's 1998 list of impaired waters Source: U.S. 
Geological Survey 


Water Chemistry Overview 


Compared to other molecules of similar molecular weight, water (H2O) has 
unique physical properties including high values for melting and boiling 
point, surface tension (water’s cohesion, or “stickiness”), and capacity to 
dissolve soluble minerals, i.e., act as a solvent. These properties are related 
to its asymmetrical structure and polar nature, which means it is electrically 
neutral overall but it has a net positive charge on the side with the two 
hydrogen atoms and a net negative charge on the oxygen side ({link]). This 
separation of the electrical charge within a water molecule results in 
hydrogen bonds with other water molecules, mineral surfaces (hydrogen 
bonding produces the water films on minerals in the unsaturated zone of the 
subsurface), and dissolved ions (atoms with a negative or positive charge). 
Many minerals and pollutants dissolve readily in water because water forms 


hydration shells (spheres of loosely coordinated, oriented water molecules) 
around ions. 


Hydrogen 
bonds 


Structure of Water, Polar Charge of Water, 
and Hydrogen Bonds between Water 
Molecules Source: Michal Maras at 
Wikimedia Commons 


Any natural water contains dissolved chemicals; some of these are 
important human nutrients, while others can be harmful to human health. 
The abundance of a water pollutant is commonly given in very small 
concentration units such as parts per million (ppm) or even parts per billion 
(ppb). An arsenic concentration of 1 ppm means 1 part of arsenic per 
million parts of water. This is equivalent to one drop of arsenic in 50 liters 


of water. To give you a different perspective on appreciating small 
concentration units, converting 1 ppm to length units is 1 cm (0.4 in) in 10 
km (6 miles) and converting 1 ppm to time units is 30 seconds in a year. 
Total dissolved solids (TDS) represent the total amount of dissolved 
material in water. Average TDS (salinity) values for rainwater, river water, 
and seawater are about 4 ppm, 120 ppm, and 35,000 ppm. The most 
important processes that affect the salinity of natural waters are 
evaporation, which distills nearly pure water and leaves the dissolved ions 
in the original water, and chemical weathering, which involves mineral 
dissolution that adds dissolved ions to water. Fresh water is commonly 
defined as containing less than either 1,000 or 500 ppm TDS, but the US 
Environmental Protection Agency (EPA) recommends that drinking water 
not exceed 500 ppm TDS or else it will have an unpleasant salty taste. 


Water Pollution Overview 


Water pollution is the contamination of water by an excess amount of a 
substance that can cause harm to human beings and the ecosystem. The 
level of water pollution depends on the abundance of the pollutant, the 
ecological impact of the pollutant, and the use of the water. Pollutants are 
derived from biological, chemical, or physical processes. Although natural 
processes such as volcanic eruptions or evaporation sometimes can cause 
water pollution, most pollution is derived from human, land-based activities 
(see Figure [link]). Water pollutants can move through different water 
reservoirs, as the water carrying them progresses through stages of the 
water cycle (see Figure [link]). Water residence time (the average time that 
a water molecule spends in a water reservoir) is very important to pollution 
problems because it affects pollution potential. Water in rivers has a 
relatively short residence time, so pollution usually is there only briefly. Of 
course, pollution in rivers may simply move to another reservoir, such as 
the ocean, where it can cause further problems. Groundwater is typically 
characterized by slow flow and longer residence time, which can make 
groundwater pollution particularly problematic. Finally, pollution residence 
time can be much greater than the water residence time because a pollutant 
may be taken up for a long time within the ecosystem or absorbed onto 
sediment. 


Water Pollution Obvious water pollution in 
the form of floating debris; invisible water 
pollutants sometimes can be much more 
harmful than visible ones. Source: Stephen 
Codrington at Wikimedia Commons 


Point-source contamination can ution spreads across the landscape 


be traced to specific points of en overlooked as a major nonpoint 
discharge from wastewater of pollution. Airborne nutrients and 
treatment plants and factories or can be transported far from their 
from combined sewers. area of origin. 


atte 


soil and sediment 
transport considerable 
amounts of some nutrients, 


ciel such as organic nitrogen and 
phosphorus, and some 
pesticides, such as DDT, 
to rivers and streams. 
SEEPAGE GROUND-WATER SEEPAGE 
DISCHARGE 
TO STREAMS 


Sources of Water Contamination Sources of some water pollutants 
and movement of pollutants into different water reservoirs of the water 
cycle. Source: U.S. Geological Survey 


Pollutants enter water supplies from point sources, which are readily 
identifiable and relatively small locations, or nonpoint sources, which are 
large and more diffuse areas. Point sources of pollution include animal 
“factory” farms that raise a large number and high density of livestock such 
as cows, pigs, and chickens ([link]) and discharge pipes from a factories or 
sewage treatment plants. Combined sewer systems that have a single set of 
underground pipes to collect both sewage and storm water runoff from 
streets for wastewater treatment can be major point sources of pollutants. 
During heavy rain, storm water runoff may exceed sewer capacity, causing 
it to back up and spilling untreated sewage into surface waters ((link]). 
Nonpoint sources of pollution include agricultural fields, cities, and 
abandoned mines. Rainfall runs over the land and through the ground, 


picking up pollutants such as herbicides, pesticides, and fertilizer from 
agricultural fields and lawns; oil, antifreeze, car detergent, animal waste, 
and road salt from urban areas; and acid and toxic elements from 
abandoned mines. Then, this pollution is carried into surface water bodies 
and groundwater. Nonpoint source pollution, which is the leading cause of 
water pollution in the U.S., is usually much more difficult and expensive to 
control than point source pollution because of its low concentration, 
multiple sources, and much greater volume of water. 


hte 
pgs 
ys vz 
ae 


A Commercial Meat Chicken Production House This chicken 
factory farm is a possible major point source of water pollution. 
Source: Larry Rana at Wikimedia Commons 


Dry Weather 


Spay 


Outfall pipe and storm Wee 


to river 


Sewer to POTW 


Combined Sewer System A combined sewer system is a possible 
major point source of water pollution during heavy rain due to 
overflow of untreated sewage. During dry weather (and small storms), 
all flows are handled by the publicly owned treatment works (POTW). 
During large storms, the relief structure allows some of the combined 
stormwater and sewage to be discharged untreated to an adjacent water 
body. Source: U.S. Environmental Protection Agency at Wikimedia 
Commons 


Types of Water Pollutants 


Oxygen-demanding waste is an extremely important pollutant to 
ecosystems. Most surface water in contact with the atmosphere has a small 
amount of dissolved oxygen, which is needed by aquatic organisms for 
cellular respiration. Bacteria decompose dead organic matter (chemically 
represented in a simplified way as CH»O) and remove dissolved oxygen 
(O>) according to the following reaction: 

Equation: 


CH,0 + O2 + CO, + H2O 


Too much decaying organic matter in water is a pollutant because it 
removes oxygen from water, which can kill fish, shellfish, and aquatic 
insects. The amount of oxygen used by aerobic (in the presence of oxygen) 
bacterial decomposition of organic matter is called biochemical oxygen 
demand (BOD). The major source of dead organic matter in most natural 
waters is sewage; grass and leaves are smaller sources. An unpolluted water 
body with respect to oxygen is a turbulent river that flows through a natural 
forest. Turbulence continually brings water in contact with the atmosphere 
where the O> content is restored. The dissolved oxygen content in such a 
river ranges from 10 to 14 ppm Op», BOD is low, and clean-water fish, e.g., 
bass, trout, and perch dominate. A polluted water body with respect to 
oxygen is a stagnant deep lake in an urban setting with a combined sewer 
system. This system favors a high input of dead organic carbon from 
sewage overflows and limited chance for water circulation and contact with 
the atmosphere. In such a lake, the dissolved O, content is <5 ppm Op, 
BOD is high, and low O>-tolerant fish, e.g., carp and catfish dominate. 


Excessive plant nutrients, particularly nitrogen (N) and phosphorous (P), 
are pollutants closely related to oxygen-demanding waste. Aquatic plants 
require about 15 nutrients for growth, most of which are plentiful in water. 
N and P are called limiting nutrients, because they usually are present in 
water at low concentrations and therefore restrict the total amount of plant 
growth. This explains why N and P are major ingredients in most fertilizer. 
High concentrations of N and P from human sources (mostly agricultural 
and urban runoff including fertilizer, sewage, and P-based detergent) can 
cause cultural eutrophication, which involves the rapid growth of aquatic 
plants, particularly algae, called an algal bloom. Thick mats of floating and 
rooted green or sometimes red algae ([link]) create water pollution, damage 
the ecosystem by clogging fish gills and blocking sunlight, and damage lake 
aesthetics by making recreation difficult and creating an eyesore. A small 
percentage of algal species produce toxins that can kill fish, mammals, and 
birds, and may cause human illness; explosive growths of these algae are 
called harmful algal blooms ({link]). When the prolific algal layer dies, it 
becomes oxygen-demanding waste, which can create very low O> water 
(<~2 ppm O>), called hypoxia or dead zone because it causes death to 
organisms that are unable to leave that environment. An estimated 50% of 
lakes in North America, Europe, and Asia are negatively impacted by 


cultural eutrophication. In addition, the size and number of marine hypoxic 
zones have grown dramatically over the past 50 years ({link]), including a 
very large dead zone located offshore Louisiana in the Gulf of Mexico. 
Cultural eutrophication and hypoxia are difficult to combat, because they 
are caused primarily by nonpoint source pollution, which is difficult to 
regulate, and N and P, which are difficult to remove from wastewater. 


Algal Bloom in River in Sichuan, China Algal 
blooms can present problems for ecosystems and 
human society. Source: Felix Andrews via Wikimedia 
Commons 


Harmful Algal Bloom Harmful algal bloom with deep red color. 
Source: Kai Schumann via National Oceanic and Atmospheric 
Administration 


Particulate Organic Carbon pam Poputation Density (persoris/em') 


S aaa 
0 23 0 103 200 $00 1,000 ' 10 100 1,000 FOR 100K 


Dead Zone Size (my) 
nouns « ee 
O1 4 10 100 1k 108 


Aquatic Dead Zones Zones of hypoxia shown as red circles. Black 
dots show hypoxia zones of unknown size, brown shading shows 
population density, and blue shading shows density of particulate 

organic carbon, an indicator of organic productivity. Source: Robert 
Simmon & Jesse Allen at NASA Earth Observatory via Wikimedia 

Commons 


Pathogens are disease-causing microorganisms, e.g., viruses, bacteria, 
parasitic worms, and protozoa, which cause a variety of intestinal diseases 
such as dysentery, typhoid fever, hepatitis, and cholera. Pathogens are the 
major cause of the water pollution crisis discussed at the beginning of this 
section. Unfortunately nearly a billion people around the world are exposed 
to waterborne pathogen pollution daily and around 1.5 million children 
mainly in underdeveloped countries die every year of waterborne diseases 
from pathogens. Pathogens enter water primarily from human and animal 
fecal waste due to inadequate sewage treatment. In many underdeveloped 
countries, sewage is discharged into local waters either untreated or after 


only rudimentary treatment. In developed countries untreated sewage 
discharge can occur from overflows of combined sewer systems, poorly 
managed livestock factory farms, and leaky or broken sewage collection 
systems. Water with pathogens can be remediated by adding chlorine or 
ozone, by boiling, or by treating the sewage in the first place. 


Oil spills are another kind of organic pollution. Oil spills can result from 
supertanker accidents such as the Exxon Valdez in 1989, which spilled 10 
million gallons of oil into the rich ecosystem of offshore south Alaska and 
killed massive numbers of animals. The largest marine oil spill was the 
Deepwater Horizon disaster, which began with a natural gas explosion (see 
Figure [link]) at an oil well 65 km offshore of Louisiana and flowed for 3 
months in 2010, releasing an estimated 200 million gallons of oil. The 
worst oil spill ever occurred during the Persian Gulf war of 1991, when Iraq 
deliberately dumped approximately 200 million gallons of oil in offshore 
Kuwait and set more than 700 oil well fires that released enormous clouds 
of smoke and acid rain for over nine months. During an oil spill on water, 
oil floats to the surface because it is less dense than water, and the lightest 
hydrocarbons evaporate, decreasing the size of the spill but polluting the air. 
Then, bacteria begin to decompose the remaining oil, in a process that can 
take many years. After several months only about 15% of the original 
volume may remain, but it is in thick asphalt lumps, a form that is 
particularly harmful to birds, fish, and shellfish. Cleanup operations can 
include skimmer ships that vacuum oil from the water surface (effective 
only for small spills), controlled burning (works only in early stages before 
the light, ignitable part evaporates but also pollutes the air), dispersants 
(detergents that break up oil to accelerate its decomposition, but some 
dispersants may be toxic to the ecosystem), and bioremediation (adding 
microorganisms that specialize in quickly decomposing oil, but this can 
disrupt the natural ecosystem). 


Deepwater Horizon Explosion Boats fighting the fire from an 
explosion at the Deepwater Horizon drilling ng 1 in ee oe ioe 
offshore Louisiana on April 20, 2010. Source: States Coast 

suard via Wikimedia Commons 


Toxic chemicals involve many different kinds and sources, primarily from 
industry and mining. General kinds of toxic chemicals include hazardous 
chemicals, which are a wide variety of synthetic organic and inorganic 
chemicals such as acids, bases, cyanide, and a class of compounds called 
persistent organic pollutants that includes DDT (pesticide), dioxin 
(herbicide by-product), and PCBs (polychlorinated biphenyls, which were 
used as a liquid insulator in electric transformers). Persistent organic 
pollutants are long-lived in the environment, accumulate through the food 


chain (bioaccumulation), and can be toxic. Another category of toxic 
chemicals includes radioactive materials such as cesium, iodine, uranium, 
and radon gas, which can result in long-term exposure to radioactivity if it 
gets into the body. A final group of toxic chemicals is heavy metals such as 
lead, mercury, arsenic, cadmium, and chromium, which can accumulate 
through the food chain. Heavy metals are commonly produced by industry 
and at metallic ore mines. Arsenic and mercury are discussed in more detail 
below. The US EPA regulates 83 contaminants in drinking water to ensure a 
safe public water supply. Similarly, at the international level the World 
Health Organization has drinking water standards for a variety of 
contaminants. 


Arsenic (As) has been famous as an agent of death for many centuries. In 
large doses arsenic causes cancer and can be fatal. Only recently have 
scientists recognized that health problems can be caused by drinking small 
arsenic concentrations in water over a long time. It attacks the central 
nervous system and can damage the respiratory system, bladder, lungs, 
liver, and kidneys. It enters the water supply naturally from weathering of 
As-rich minerals and from human activities such as coal burning and 
smelting of metallic ores. The worst case of arsenic poisoning occurred in 
the densely populated impoverished country of Bangladesh, which had 
experienced 100,000s of deaths from diarrhea and cholera each year from 
drinking surface water contaminated with pathogens due to improper 
sewage treatment. In the 1970s the United Nations provided aid for millions 
of shallow water wells, which resulted in a dramatic drop in pathogenic 
diseases. Unfortunately, many of the wells produced water naturally rich in 
arsenic. Tragically, there are an estimated 77 million people (about half of 
the population) who inadvertently may have been exposed to toxic levels of 
arsenic in Bangladesh as a result. The World Health Organization has called 
it the largest mass poisoning of a population in history. 


Mercury (Hg) is used in a variety of electrical products, such as dry cell 
batteries, fluorescent light bulbs, and switches, as well as in the 
manufacture of paint, paper, vinyl chloride, and fungicides. In the 
methylmercury form (CH3Hg’”) it is highly toxic; > 1 ppb of methylmercury 
represents water contaminated with mercury. Mercury and other toxic 
chemicals become concentrated in the food chain, especially in fish, in a 


process caused biological magnification ([link]). It acts on the central 
nervous system and can cause loss of sight, feeling, and hearing as well as 
nervousness, shakiness, and death. Like arsenic, mercury enters the water 
supply naturally from weathering of Hg-rich minerals and from human 
activities such as coal burning and metal processing. A famous mercury 
poisoning case in Minamata, Japan involved methylmercury-rich industrial 
discharge that caused high Hg levels in fish. People in the local fishing 
villages ate fish up to three times per day for over 30 years, which resulted 
in over 2,000 deaths. During that time the responsible company and 
national government did little to mitigate, help alleviate, or even 
acknowledge the problem. 


Biological magnification represents the processes in an ecosystem that 
cause greater concentrations of a chemical, such as methylmercury, in 
organisms higher up the food chain. Mercury and methylmercury are 
present in only very small concentrations in seawater; however, at the base 
of the food chain algae absorb methylmercury. Then, small fish eat the 
algae, large fish and other organisms higher in the food chain eat the small 
fish, and so on. Fish and other aquatic organisms absorb methylmercury 
rapidly but eliminate it slowly from the body. Therefore, each step up the 
food chain increases the concentration from the step below ((link]). 
Largemouth bass can concentrate methylmercury up to 10 million times 
over the water concentration and fish-eating birds can concentrate it even 
higher. Other chemicals that exhibit biological magnification are DDT, 
PCBs, and arsenic. 


Biological 
magnification 
An illustrative 

example of 

biological 
magnification 
of mercury 
from water 
through the 
food chain and 
into a bird's 
egg. Source: 
U.S. 
Geological 
Survey 


Other water pollutants include sediment and heat. Muddy water is bad for 
drinking but even worse for underwater plants that need sunlight for 
photosynthesis. Much of the sediment in water bodies is derived from the 
erosion of soil, so it also represents a loss of agricultural productivity. 


Thermal pollution involves the release of heated waters from power plants 
and industry to surface water, causing a drop in the dissolved O> content, 
which can stress fish. 


Hard water contains abundant calcium and magnesium, which reduces its 
ability to develop soapsuds and enhances scale (calcium and magnesium 
carbonate minerals) formation on hot water equipment. Water softeners 
remove calcium and magnesium, which allows the water to lather easily 
and resist scale formation. Hard water develops naturally from the 
dissolution of calcium and magnesium carbonate minerals in soil; it does 
not have negative health effects in people. 


Groundwater pollution can occur from underground sources and all of the 
pollution sources that contaminate surface waters. Common sources of 
groundwater pollution are leaking underground storage tanks for fuel, septic 
tanks, agricultural activity, and landfills. Common groundwater pollutants 
include nitrate, pesticides, volatile organic compounds, and petroleum 
products. Polluted groundwater can be a more serious problem than 
polluted surface water because the pollution in groundwater may go 
undetected for a long time because usually it moves very slowly. As a 
result, the pollution in groundwater may create a contaminant plume, a 
large body of flowing polluted groundwater, making cleanup very costly. 
By the time groundwater contamination is detected, the entity responsible 
for the pollution may be bankrupt or nonexistent. Another troublesome 
feature of groundwater pollution is that small amounts of certain pollutants, 
e.g., petroleum products and organic solvents, can contaminate large areas. 
In Denver, Colorado 80 liters of several organic solvents contaminated 4.5 
trillion liters of groundwater and produced a 5 km long contaminant plume. 
Most groundwater contamination occurs in shallow, unconfined aquifers 
located near the contamination source. Confined aquifers are less 
susceptible to pollution from the surface because of protection by the 
confining layer. A major threat to groundwater quality is from underground 
fuel storage tanks. Fuel tanks commonly are stored underground at gas 
stations to reduce explosion hazards. Before 1988 in the U.S. these storage 
tanks could be made of metal, which can corrode, leak, and quickly 
contaminate local groundwater. Now, leak detectors are required and the 
metal storage tanks are supposed to be protected from corrosion or replaced 


with fiberglass tanks. Currently there are around 600,000 underground fuel 
storage tanks in the U.S. and over 30% still do not comply with EPA 
regulations regarding either release prevention or leak detection. 


Contaminant Plume in Groundwater Mapping how a contaminant 
plume will migrate once it reaches groundwater requires understanding 
of the pollutant's chemical properties, local soil characteristics, and 
how permeable the aquifer is. Source: United States Geological Survey 


Sustainable Solutions to the Water Pollution Crisis? 


Resolution of the global water pollution crisis described at the beginning of 
this section requires multiple approaches to improve the quality of our fresh 
water and move towards sustainability. The most deadly form of water 
pollution, pathogenic microorganisms that cause waterborne diseases, kills 
almost 2 million people in underdeveloped countries every year. The best 


strategy for addressing this problem is proper sewage (wastewater) 
treatment. Untreated sewage is not only a major cause of pathogenic 
diseases, but also a major source of other pollutants, including oxygen- 
demanding waste, plant nutrients (N and P), and toxic heavy metals. 
Wastewater treatment is done at a sewage treatment plant in urban areas and 
through a septic tank system in rural areas. 


The main purpose of a sewage treatment plant is to remove organic matter 
(oxygen-demanding waste) and kill bacteria; special methods also can be 
used to remove plant nutrients and other pollutants. The numerous 
processing steps at a conventional sewage treatment plant ([link]) include 
pretreatment (screening and removal of sand and gravel), primary treatment 
(settling or floatation to remove organic solids, fat, and grease), secondary 
treatment (aerobic bacterial decomposition of organic solids), tertiary 
treatment (bacterial decomposition of nutrients and filtration), disinfection 
(treatment with chlorine, ozone, ultraviolet light, or bleach), and either 
discharge to surface waters (usually a local river) or reuse for some other 
purpose, such as irrigation, habitat preservation, and artificial groundwater 
recharge. The concentrated organic solid produced during primary and 
secondarytreatment is called sludge, which is treated in a variety of ways 
including landfill disposal, incineration, use as fertilizer, and anaerobic 
bacterial decomposition, which is done in the absence of oxygen. Anaerobic 
decomposition of sludge produces methane gas, which can be used as an 
energy source. To reduce water pollution problems, separate sewer systems 
(where street runoff goes to rivers and only wastewater goes to a 
wastewater treatment plant) are much better than combined sewer systems, 
which can overflow and release untreated sewage into surface waters during 
heavy rain. Some cities such as Chicago, Illinois have constructed large 
underground caverns and also use abandoned rock quarries to hold storm 
sewer overflow. After the rain stops, the stored water goes to the sewage 
treatment plant for processing. 


Steps at a Sewage Treatment Plant The numerous processing steps 
at a conventional sewage treatment plant include pretreatment 
(screening and removal of sand and gravel), primary treatment 

(settling or floatation to remove organic solids, fat, and grease), 
secondary treatment (aerobic bacterial decomposition of organic 
solids), tertiary treatment (bacterial decomposition of nutrients and 
filtration), disinfection (treatment with chlorine, ozone, ultraviolet 
light, or bleach), and either discharge to surface waters (usually a local 
river) or reuse for some other purpose, such as irrigation, habitat 
preservation, and artificial groundwater recharge. Source: Leonard 
G.via Wikipedia 


A septic tank system is an individual sewage treatment system for homes in 
rural and even some urban settings. The basic components of a septic tank 
system ([link] include a sewer line from the house, a septic tank (a large 
container where sludge settles to the bottom and microorganisms 


decompose the organic solids anaerobically), and the drain field (network of 
perforated pipes where the clarified water seeps into the soil and is further 
purified by bacteria). Water pollution problems occur if the septic tank 
malfunctions, which usually occurs when a system is established in the 
wrong type of soil or maintained poorly. 


SI udge PA Effluent 


Sewage enters To drain field 
from home and laterals 


Septic System Septic tank system for 
sewage treatment. Source: United 
States Geological Survey 


For many developing countries, financial aid is necessary to build adequate 
sewage treatment facilities; however, the World Health Organization 
estimates an estimated cost savings of between $3 and $34 for every $1 
invested in clean water delivery and sanitation (Water for Life, 2005). The 
cost savings are from health care savings, gains in work and school 
productivity, and deaths prevented. Simple and inexpensive techniques for 
treating water at home include chlorination, filters, and solar disinfection. 
Another alternative is to use constructed wetlands technology (marshes 
built to treat contaminated water), which is simpler and cheaper than a 
conventional sewage treatment plant. 


Bottled water is not a sustainable solution to the water crisis, despite 
exponential growth in popularity in the U.S. and the world. Bottled water is 
not necessarily any safer than the U.S. public water supply, it costs on 
average about 700 times more than U.S. tap water, and every year it uses 
approximately 200 billion plastic and glass bottles that have a relatively low 
rate of recycling. Compared to tap water, it uses much more energy, mainly 
in bottle manufacturing and long-distance transportation. If you don’t like 
the taste of your tap water, then please use a water filter instead of bottled 
water! 


Additional sustainable solutions to the water pollution crisis include 
legislation to eliminate or greatly reduce point sources of water pollution. In 
the U.S., the Clean Water Act of 1972 and later amendments led to major 
improvements in water quality ([link]). Nonpoint sources of water 
pollution, e.g., agricultural runoff and urban runoff, are much harder to 
regulate because of their widespread, diffuse nature. There are many 
construction and agricultural practices that reduce polluted runoff including 
no-till farming and sediment traps. Artificial aeration or mechanical mixing 
can remediate lakes with oxygen depletion. Specific things that we can do 
to reduce urban runoff include the following: keep soil, leaves, and grass 
clippings off driveways, sidewalks, and streets; don't pour used motor oil, 
antifreeze, paints, pesticides, or any household hazardous chemical down 
the storm sewer or drain; recycle used motor oil; use hazardous waste 
disposal programs offered by the community; compost your organic waste; 
don't use fertilizers and herbicides on your lawn; and flush pet waste down 
the toilet. 


During the early 1900s rapid industrialization in the U.S. resulted in 
widespread water pollution due to free discharge of waste into surface 
waters. The Cuyahoga River in northeast Ohio caught fire numerous times 
({link]), including a famous fire in 1969 that caught the nation’s attention. 
In 1972 Congress passed one of the most important environmental laws in 
U.S. history, the Federal Water Pollution Control Act, which is more 
commonly called the Clean Water Act. The purpose of the Clean Water Act 
and later amendments is to maintain and restore water quality, or in simpler 
terms to make our water swimmable and fishable. It became illegal to dump 
pollution into surface water unless there was formal permission and U.S. 
water quality improved significantly as a result. More progress is needed 
because currently the EPA considers over 40,000 U.S. water bodies as 
impaired, most commonly due to pathogens, metals, plant nutrients, and 
oxygen depletion. Another concern is protecting groundwater quality, 
which is not yet addressed sufficiently by federal law. 


Cuyahoga River on Fire Source: National Oceanic and 
Atmospheric 


Sometimes slow flow through a soil can naturally purify groundwater 
because some pollutants, such as P, pesticides, and heavy metals, 
chemically bind with surfaces of soil clays and iron oxides. Other pollutants 
are not retained by soil particles: These include N, road salt, gasoline fuel, 
the herbicide atrazine, tetrachloroethylene (a carcinogenic cleaning solvent 
used in dry cleaning), and vinyl chloride. In other cases, slow groundwater 
flow can allow bacteria to decompose dead organic matter and certain 
pesticides. There are many other ways to remediate polluted groundwater. 
Sometimes the best solution is to stop the pollution source and allow natural 
cleanup. Specific treatment methods depend on the geology, hydrology, and 
pollutant because some light contaminants flow on top of groundwater, 
others dissolve and flow with groundwater, and dense contaminants can 
sink below groundwater. A common cleanup method called pump and treat 
involves pumping out the contaminated groundwater and treating it by 
oxidation, filtration, or biological methods. Sometimes soil must be 
excavated and sent to a landfill. In-situ treatment methods include adding 
chemicals to immobilize heavy metals, creating a permeable reaction zone 
with metallic iron that can destroy organic solvents, or using bioremediation 
by adding oxygen or nutrients to stimulate growth of microorganisms. 


References 


Water for Life: Making it Happen (2005) World Health Organization and 
UNICEF. Retrieved from 
http://www.who.int/water_ sanitation health/waterforlife.pdf 


World Health Statistics (2010) World Health Organization. Retrieved from 
http://www.who.int/whosis/whostat/EN_WHS10_ Full .pdf 


Introduction to Cells 


Introduction 

"The history of the knowledge of the phenomena of life and of the 
organized world can be divided into two main periods. For a long time 
anatomy, and particularly the anatomy of the human body, was the alpha 
and omega of scientific knowledge. Further progress only became possible 
with the discovery of the microscope. A long time had yet to pass until 
through Schwann the cell was established as the final biological unit. It 
would mean bringing coals to Newcastle were I to describe here the 
immeasurable progress which biology, in all its branches, owes to the 
introduction of this concept of the cell. For this concept is the axis around 
which the whole of modern science revolves." Paul Ehrlich, "Partial Cell 
Functions", Nobel Lecture, December 11, 1908 


Ehrlich's enthusiasm for the cell is understandable. A single cell is the basic 
unit of life, and the starting point for each and every human and other 
organism on the planet. A cell is the smallest unit of a living thing. A living 
thing, whether made of one cell (like bacteria) or many cells (like a human), 
is called an organism. Thus, cells are the basic building blocks of all 
organisms, and the study of cells is at the very heart of the research 
enterprise that we call biological science. 


Several cells of one kind that interconnect with each other and perform a 
shared function form tissues, several tissues combine to form an organ 
(your stomach, heart, or brain), and several organs make up an organ 
system (such as the digestive system, circulatory system, or nervous 
system). Several systems that function together form an organism (like a 
human being). Here, we will examine the structure and function of cells. 


There are many types of cells, all grouped into one of two broad categories: 
prokaryotic and eukaryotic. For example, both animal and plant cells are 
classified as eukaryotic cells, whereas bacterial cells are classified as 
prokaryotic. Before discussing the criteria for determining whether a cell is 
prokaryotic or eukaryotic, let’s first examine how biologists study cells. 


Microscopy 


Cells vary in size. With few exceptions, individual cells cannot be seen with 
the naked eye, so scientists use microscopes (micro- = “small”; -scope = “to 
look at”) to study them. A microscope is an instrument that magnifies an 
object. Most photographs of cells are taken with a microscope, and these 
images can also be called micrographs. 


The optics of a microscope’s lenses change the orientation of the image that 
the user sees. A specimen that is right-side up and facing right on the 
microscope slide will appear upside-down and facing left when viewed 
through a microscope, and vice versa. Similarly, if the slide is moved left 
while looking through the microscope, it will appear to move right, and if 
moved down, it will seem to move up. This occurs because microscopes use 
two sets of lenses to magnify the image. Because of the manner by which 
light travels through the lenses, this system of two lenses produces an 
inverted image (binocular, or dissecting microscopes, work in a similar 
manner, but include an additional magnification system that makes the final 
image appear to be upright). 


Light Microscopes 


To give you a sense of cell size, a typical human red blood cell is about 
eight millionths of a meter or eight micrometers (abbreviated as eight 1m, 
or eight 1) in diameter; the head of a pin of is about two thousandths of a 
meter (two mm) in diameter. That means about 250 red blood cells could fit 
on the head of a pin. 


Most student microscopes are classified as light microscopes ((link]a). 
Visible light passes and is bent through the lens system to enable the user to 
see the specimen. Light microscopes are advantageous for viewing living 
organisms, but since individual cells are generally transparent, their 
components are not distinguishable unless they are colored with special 
stains. Staining, however, usually kills the cells. 


Light microscopes commonly used in the undergraduate college laboratory 
magnify up to approximately 400 times. Two parameters that are important 
in microscopy are magnification and resolving power. Magnification is the 


process of enlarging an object in appearance. Resolving power is the ability 
of a microscope to distinguish two adjacent structures as separate: the 
higher the resolution, the better the clarity and detail of the image. When oil 
immersion lenses are used for the study of small objects, magnification is 
usually increased to 1,000 times. In order to gain a better understanding of 
cellular structure and function, scientists typically use electron microscopes. 


(a) Most light microscopes used 
in a college biology lab can 
magnify cells up to 
approximately 400 times and 
have a resolution of about 200 
nanometers. (b) Electron 
microscopes provide a much 
higher magnification, 100,000x, 
and a have a resolution of 50 
picometers. (credit a: 
modification of work by 
"GcG"/Wikimedia Commons; 
credit b: modification of work 
by Evan Bench) 


Electron Microscopes 


In contrast to light microscopes, electron microscopes ({link]|b) use a beam 
of electrons instead of a beam of light. Not only does this allow for higher 
magnification and, thus, more detail ([link]), it also provides higher 
resolving power. The method used to prepare the specimen for viewing with 
an electron microscope kills the specimen. Electrons have short 
wavelengths (shorter than photons) that move best in a vacuum, so living 
cells cannot be viewed with an electron microscope. 


In a scanning electron microscope, a beam of electrons moves back and 
forth across a cell’s surface, creating details of cell surface characteristics. 
In a transmission electron microscope, the electron beam penetrates the cell 
and provides details of a cell’s internal structures. As you might imagine, 
electron microscopes are significantly more bulky and expensive than light 
microscopes. 


(a) These Salmonella bacteria appear as tiny 
purple dots when viewed with a light 
microscope. (b) This scanning electron 
microscope micrograph shows Salmonella 
bacteria (in red) invading human cells 
(yellow). Even though subfigure (b) shows a 
different Salmonella specimen than 
subfigure (a), you can still observe the 
comparative increase in magnification and 
detail. (credit a: modification of work by 
CDC/Armed Forces Institute of Pathology, 


Charles N. Farmer, Rocky Mountain 
Laboratories; credit b: modification of work 
by NIAID, NIH; scale-bar data from Matt 
Russell) 


Cell Theory 


The microscopes we use today are far more complex than those used in the 
1600s by Antony van Leeuwenhoek, a Dutch shopkeeper who had great 
skill in crafting lenses. Despite the limitations of his now-ancient lenses, 
van Leeuwenhoek observed the movements of protista (a type of single- 
celled organism) and sperm, which he collectively termed “animalcules.” 


In a 1665 publication called Micrographia, experimental scientist Robert 
Hooke coined the term “cell” for the box-like structures he observed when 
viewing cork tissue through a lens. In the 1670s, van Leeuwenhoek 
discovered bacteria and protozoa. Later advances in lenses, microscope 
construction, and staining techniques enabled other scientists to see some 
components inside cells. 


By the late 1830s, botanist Matthias Schleiden and zoologist Theodor 
Schwann were studying tissues and proposed the unified cell theory, which 
States that all living things are composed of one or more cells, the cell is the 
basic unit of life, and new cells arise from existing cells. Rudolf Virchow 
later made important contributions to this theory. 


Note: 

Career Connection 

Cytotechnologist 

Have you ever heard of a medical test called a Pap smear ((link])? In this 
test, a doctor takes a small sample of cells from the uterine cervix of a 
patient and sends it to a medical lab where a cytotechnologist stains the 


cells and examines them for any changes that could indicate cervical 
cancer or a microbial infection. 

Cytotechnologists (cyto- = “cell”) are professionals who study cells via 
microscopic examinations and other laboratory tests. They are trained to 
determine which cellular changes are within normal limits and which are 
abnormal. Their focus is not limited to cervical cells; they study cellular 
specimens that come from all organs. When they notice abnormalities, they 
consult a pathologist, who is a medical doctor who can make a clinical 
diagnosis. 

Cytotechnologists play a vital role in saving people’s lives. When 
abnormalities are discovered early, a patient’s treatment can begin sooner, 
which usually increases the chances of a successful outcome. 


“a 


These uterine cervix cells, viewed 
through a light microscope, were 
obtained from a Pap smear. 
Normal cells are on the left. The 
cells on the right are infected with 
human papillomavirus (HPV). 
Notice that the infected cells are 
larger; also, two of these cells 
each have two nuclei instead of 
one, the normal number. (credit: 
modification of work by Ed 
Uthman, MD; scale-bar data from 
Matt Russell) 


The Phylogenetic Relationship of Life 


All of life can be grouped into three Domains Archaea, Bacteria and 
Eukarya ({link]). Even though Archaea and Bacteria are prokaryotes, there 
are enough differences between Archaea and Bacteria that warrant them 
being in different Domains. Within the Domain Eukarya, there are at least 
four Kingdoms Protists (multiple kingdoms), Fungi, Plantae and Animalia. 
Figure 4 shows the current phylogentic tree of all these various groups that 
we will be exploring. 


Bacteria Archaea Eukarya 


Animals 
Fungi 


Plants 


Protista 


The phylogenetic tree of the Domains Bacteria, Archeae 
and the four Kingdoms of Eukarya. Work by Eva Horne 


Our approach to Cell Biology 


In this textbook, we explore cells and the chemistry of life in the reverse 
order of many traditional textbooks. First, we explore the diversity of life at 


the cellular level and then we investigate the chemistry of life or 
Biochemistry. The reason why we take this approach is based on the fact 
that many students have had some exposure to cells and this exposure 
allows them to connect with the material. In addition, we feel a macro to 
micro approach to investigating this material allows the learner the ability 
to better connect how the biochemistry relates to the functioning cell. 


Prokaryotic Cells 


Introduction 

"With the identification and characterization of the kingdoms we are for the 
first time beginning to see the overall phylogenetic structure of the living 
world. It is not structured in a bipartite way along the lines of the 
organizationally dissimilar prokaryote and eukaryote. Rather, it is (at least) 
tripartite, comprising (i) the typical bacteria, (ii) the line of descent 
manifested in eukaryotic cytoplasms, and (iii) a little explored grouping, 
represented so far only by methanogenic bacteria." Cal Woese and George 
Fox, "Phylogenetic structure of the prokaryotic domain: the primary 
kingdoms", Proceedings of the National Academy of Science, USA. 1977 
74(11):5088-90. 


Cells fall into one of two broad categories: prokaryotic and eukaryotic. 
Until the publication of the paper cited above, it was believed that the 
prokaryotic cells were all members of the group we know as Bacteria. 
Woese and Fox (and others) laid out a strong case for another class of 
prokaryotic cells, which they christened the Archaea. Cells of animals, 
plants, fungi, and protists are all eukaryotes (eu- = “true”, karyo = 
"nucleus") and are made up of eukaryotic cells. The single-celled organisms 
of the domains Bacteria and Archaea are prokaryotes (pro- = “before”). We 
will consider these two domains here, since they have some similarities, but 
it is good to remember that Bacteria and Archea are as different from each 
other as they are different from the Eukaryotes. 


Components of Prokaryotic Cells 


All cells share four common components: 1) a plasma membrane, an outer 
covering that separates the cell’s interior from its surrounding environment; 
2) cytoplasm, consisting of a jelly-like cytosol within the cell in which other 
cellular components are found; 3) DNA, the genetic material of the cell; and 
4) ribosomes, which synthesize proteins. However, prokaryotes differ from 
eukaryotic cells in several ways. 


A prokaryote is a simple, mostly single-celled (unicellular) organism that 
lacks a nucleus, or any other membrane-bound organelle. We will shortly 


come to see that this is significantly different in eukaryotes. Prokaryotic 
DNA is found in a central part of the cell: the nucleoid ([link)). 


Plasma 


Flagellum 


Chromosomal DNA is 
localized in a region 
called the nucleoid. 


This figure shows the generalized 
structure of a prokaryotic cell. All 
prokaryotes have chromosomal DNA 
localized in a nucleoid, ribosomes, a 
plasma membrane, and a cell wall. 
The other structures shown are present 
in some, but not all, bacteria. 


Most prokaryotes have a peptidoglycan cell wall and many have a 
polysaccharide capsule ({link]). The cell wall acts as an extra layer of 
protection, helps the cell maintain its shape, and prevents dehydration. The 
capsule enables the cell to attach to surfaces in its environment. Some 
prokaryotes have flagella, pili, or fimbriae. Flagella are used for 
locomotion. Pili are used to exchange genetic material during a type of 
reproduction called conjugation. Fimbriae are used by bacteria to attach to a 
host cell. 


Note: 

Career Connection 

Microbiologist 

The most effective action anyone can take to prevent the spread of 
contagious illnesses is to wash his or her hands. Why? Because microbes 
(organisms so tiny that they can only be seen with microscopes) are 
ubiquitous. They live on doorknobs, money, your hands, and many other 
surfaces. If someone sneezes into his hand and touches a doorknob, and 
afterwards you touch that same doorknob, the microbes from the sneezer’s 
mucus are now on your hands. If you touch your hands to your mouth, 
nose, or eyes, those microbes can enter your body and could make you 
sick. 

However, not all microbes (also called microorganisms) cause disease; 
most are actually beneficial. You have microbes in your gut that make 
vitamin K. Other microorganisms are used to ferment beer and wine. 
Microbiologists are scientists who study microbes. Microbiologists can 
pursue a number of careers. Not only do they work in the food industry, 
they are also employed in the veterinary and medical fields. They can work 
in the pharmaceutical sector, serving key roles in research and 
development by identifying new sources of antibiotics that could be used 
to treat bacterial infections. 

Environmental microbiologists may look for new ways to use specially 
selected or genetically engineered microbes for the removal of pollutants 
from soil or groundwater, as well as hazardous elements from 
contaminated sites. These uses of microbes are called bioremediation 
technologies. Microbiologists can also work in the field of bioinformatics, 
providing specialized knowledge and insight for the design, development, 
and specificity of computer models of, for example, bacterial epidemics. 


Cell Size 


At 0.1 to 5.0 um in diameter, prokaryotic cells are significantly smaller than 
eukaryotic cells, which have diameters ranging from 10 to 100 um ([Link)). 
The small size of prokaryotes allows ions and organic molecules that enter 
them to quickly diffuse to other parts of the cell. Similarly, any wastes 


produced within a prokaryotic cell can quickly diffuse out. This is not the 
case in eukaryotic cells, which have developed different structural 
adaptations to enhance intracellular transport. 


Animal 
cell 


Mitochondria 


Protein 


i) 


Lipids Ostrich Adult 
Bacteria egg female 


0.1 nm inm 10 nm 100 nm tum 10 um 100 um 1mm 10 mm 100 mm 1m 


Naked eye 


td 


Light microscope 


Electron microscope 


This figure shows relative sizes of microbes on a logarithmic scale 
(recall that each unit of increase in a logarithmic scale represents a 
10-fold increase in the quantity being measured). 


Small size, in general, is necessary for all cells, whether prokaryotic or 
eukaryotic. Let’s examine why that is so. First, we’ ll consider the area and 
volume of a typical cell. Not all cells are spherical in shape, but most tend 
to approximate a sphere. You may remember from your high school 
geometry course that the formula for the surface area of a sphere is 4mr?, 
while the formula for its volume is 4mr?/3. Thus, as the radius of a cell 
increases, its surface area increases as the square of its radius, but its 
volume increases as the cube of its radius (much more rapidly). Therefore, 


as a Cell increases in size, its surface area-to-volume ratio decreases. This 
same principle would apply if the cell had the shape of a cube ({link]). If the 
cell grows too large, the plasma membrane will not have sufficient surface 
area to support the rate of diffusion required for the increased volume. In 
other words, as a cell grows, it becomes less efficient. One way to become 
more efficient is to divide; another way is to develop organelles that 
perform specific tasks. These adaptations lead to the development of more 
sophisticated cells called eukaryotic cells. 


Notice that as a cell increases in size, 
its surface area-to-volume ratio 
decreases. When there is insufficient 
surface area to support a cell’s 
increasing volume, a cell will either 
divide or die. The cell on the left has a 
volume of 1 mm? and a surface area 
of 6 mm2, with a surface area-to- 
volume ratio of 6 to 1, whereas the 
cell on the right has a volume of 8 
mm? and a surface area of 24 mm?, 
with a surface area-to-volume ratio of 
3 to 1. 


Eukaryotic Cells 


Introduction 

"The cell, too, has a geography. And its reactions occur in a colloidal 
apparatus, of which the form, and the catalytic activity of its manifold 
surfaces, must efficiently contribute to the due guidance of chemical 
reactions. " Frederick C. Hopkins, "Some Aspects of Biochemistry", The 
Trish Journal of Medical Science, 1932, 79:344 


Have you ever heard the phrase “form follows function?” It’s a philosophy 
practiced in many industries. In architecture, this means that buildings 
should be constructed to support the activities that will be carried out inside 
them. For example, a skyscraper should be built with several elevator 
banks; a hospital should be built so that its emergency room is easily 
accessible. 


Our natural world also utilizes the principle of form following function, 
especially in cell biology, and this will become clear as we explore 
eukaryotic cells ( [link]). Unlike prokaryotic cells, eukaryotic cells have: 1) 
a membrane-bound nucleus; 2) numerous membrane-bound organelles 
such as the endoplasmic reticulum, Golgi apparatus, chloroplasts, 
mitochondria, and others; and 3) several, rod-shaped chromosomes. Of 
these, Hopkins points out the membrane systems (the "manifold surfaces") 
as being especially important. Indeed, the study of eukaryotic cells is in 
many respects the study of the structure and function of these surfaces. 
Different organelles have different forms and functions based on the form 
and function of their component membranes. Indeed, the word “organelle” 
means “little organ,” and organelles have specialized shapes and specialized 
functions, just as the organs of your body have specialized shapes and 
functions. 


At this point, it should be clear to you that eukaryotic cells have a more 
complex structure than prokaryotic cells. Organelles allow different 
functions to be compartmentalized in different areas of the cell. Before 
turning to organelles, let’s first examine two important components of the 
cell: the plasma membrane and the cytoplasm. 


These figures show the major organelles and other cell components of 
(a) a typical animal cell and (b) a typical eukaryotic plant cell. The 
plant cell has a cell wall, chloroplasts, plastids, and a central vacuole— 
structures not found in animal cells. Plant cells do not have lysosomes 
or centrosomes. 


Nucleus Cytoskeleton 
Nuclear envelope: Microtubules: form the 
membrane enclosing | mitotic spindle and 
the nucleus. Protein-lined maintain cell shape. 
pores allow material to Centrosome: microtubule- 
move in and out. organizing center. 
Chromatin: DNA plus Intermediate filaments: 
associated proteins. fibrous proteins that hold 
Nucleolus: organelles in place. 


condensed region Microfilaments: 
where ribosomes fibrous proteins; 


are formed. form the cellular 
Peroxisome: PI 
metabolizes peat 
waste membrane 
Lysosome: 
digests food. 
Golgi apparatus: 
modifies proteins. 
Endoplasmic I 
: m 
reticulum Cylopiss 


Rough: associated 
with ribosomes; 
makes secretory and 
membrane proteins. 
Smooth: makes lipids. 


Plasmodesmata: Endoplasmic reticulum Nucleus: contains 
channels connect smooth rough chromatin and a 
two plant cells nucleolus as in 

an animal cell 


Mitochondria: 
produce energy. 


Endosome 


Cell wall: maintains 
cell shape 


Plasma 
membrane 


Cytoplasm 
= Ribosomes 
Central vacuole: 
filled with cell sap 
that maintains 
pressure against 
cell wall 


Golgi 
apparatus 


Mitochondria 


Cytoskeleton: 
microtubules 
intermediate 
filaments Chloroplast: site Plastid: stores 
microfilaments of photosynthesis pigments 


Peroxisome 


The Plasma Membrane 


Like prokaryotes, eukaryotic cells have a plasma membrane ( [link]), a 
phospholipid bilayer with embedded proteins that separates the internal 
contents of the cell from its surrounding environment. A phospholipid is a 
lipid molecule with two fatty acid chains and a phosphate-containing group. 
The plasma membrane controls the passage of organic molecules, ions, 
water, and oxygen into and out of the cell. Wastes (such as carbon dioxide 
and ammonia) also leave the cell by passing through the plasma membrane. 
Thus, the plasma membrane is said to be semi-permeable 


Glycoprotein: protein with Glycolipid: lipid with 
—. carbohydrate attached is carbohydrate 
attached 


Peripheral membrane Phospholipid 
protein bilayer 
Integral membrane Chotessarct Protein channel 
protein 


Filaments of the cytoskeleton 


The eukaryotic plasma membrane is a phospholipid bilayer with 
proteins and cholesterol embedded in it. 


The plasma membranes of cells that specialize in absorption are folded into 
fingerlike projections called microvilli (singular = microvillus); ( [link]). 
Such cells are typically found lining the small intestine, the organ that 
absorbs nutrients from digested food. This is an excellent example of form 
following function. People with celiac disease have an immune response to 
gluten, which is a protein found in wheat, barley, and rye. The immune 


response damages microvilli, and thus, afflicted individuals cannot absorb 
nutrients. This leads to malnutrition, cramping, and diarrhea. Patients 
suffering from celiac disease must follow a gluten-free diet. 


Microvilli 


Side of 
cell facing 
inside of 
small 
intestine 


Plasma membrane Nucleus 


Microvilli, shown here as they appear on cells lining the small 
intestine, increase the surface area available for absorption. These 
microvilli are only found on the area of the plasma membrane that 

faces the cavity from which substances will be absorbed. (credit 
"micrograph": modification of work by Louisa Howard) 


The Cytoplasm 


The cytoplasm is the entire region of a cell between the plasma membrane 
and the nuclear envelope (a structure to be discussed shortly). It is made up 
of organelles suspended in the gel-like cytosol, the cytoskeleton, and 
various chemicals ( [link]). Even though the cytoplasm consists of 70 to 80 
percent water, it has a semi-solid consistency, which comes from the 
proteins within it. However, proteins are not the only organic molecules 
found in the cytoplasm. Glucose and other simple sugars, polysaccharides, 
amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found 
there, too. Ions of sodium, potassium, calcium, and many other elements are 


also dissolved in the cytoplasm. Many metabolic reactions, including 
protein synthesis, take place in the cytoplasm. 


The Nucleus 


Typically, the nucleus is the most prominent organelle in a cell ( [link]). The 
nucleus (plural = nuclei) houses the cell’s DNA and directs the synthesis of 
ribosomes and proteins. Let’s look at it in more detail ( [link]). 


Endoplasmic 
reticulum 


Nucleolus 
Chromatin 
Nucleoplasm 
Nuclear pore 


Nuclear envelope 


The nucleus stores chromatin (DNA 
plus proteins) in a gel-like substance 
called the nucleoplasm. The nucleolus 
is a condensed region of chromatin 
where ribosome synthesis occurs. The 
boundary of the nucleus is called the 
nuclear envelope. It consists of two 
phospholipid bilayers: an outer 
membrane and an inner membrane. 
The nuclear membrane is continuous 
with the endoplasmic reticulum. 
Nuclear pores allow substances to 
enter and exit the nucleus. 


The Nuclear Envelope 


The nuclear envelope is a double-membrane structure that constitutes the 
outermost portion of the nucleus ( [link]). Both the inner and outer 
membranes of the nuclear envelope are phospholipid bilayers. 


The nuclear envelope is punctuated with pores that control the passage of 
ions, molecules, and RNA between the nucleoplasm and cytoplasm. The 
nucleoplasm is the semi-solid fluid inside the nucleus, where we find the 
chromatin and the nucleolus. 


Chromatin and Chromosomes 


To understand chromatin, it is helpful to first consider chromosomes. 
Chromosomes are structures within the nucleus that are made up of DNA, 
the hereditary material. You may remember that in prokaryotes, DNA is 
organized into a single circular chromosome. In eukaryotes, chromosomes 
are linear structures. Every eukaryotic species has a specific number of 
chromosomes in the nuclei of its body’s cells. For example, in humans, the 
chromosome number is 46, while in fruit flies, it is eight. Chromosomes are 
only visible and distinguishable from one another when the cell is getting 
ready to divide. When the cell is in the growth and maintenance phases of 
its life cycle, proteins are attached to chromosomes, and they resemble an 
unwound, jumbled bunch of threads. These unwound protein-chromosome 
complexes are called chromatin ( [link]); chromatin describes the material 
that makes up the chromosomes both when condensed and decondensed. 


Zz 3 
\ 
aT 


Histone: a protein associated 
with DNA 


(a) This image shows various levels of the 
organization of chromatin (DNA and protein). (b) 
This image shows paired chromosomes. (credit b: 
modification of work by NIH; scale-bar data from 

Matt Russell) 


The Nucleolus 


We already know that the nucleus directs the synthesis of ribosomes, but 
how does it do this? Some chromosomes have sections of DNA that encode 
ribosomal RNA. A darkly staining area within the nucleus called the 
nucleolus (plural = nucleoli) aggregates the ribosomal RNA with associated 
proteins to assemble the ribosomal subunits that are then transported out 
through the pores in the nuclear envelope to the cytoplasm. 


Ribosomes 


Ribosomes are the cellular organelles responsible for protein synthesis. 
When viewed through an electron microscope, ribosomes appear either as 
clusters (polyribosomes) or single, tiny dots that float freely in the 
cytoplasm. They may be attached to the cytoplasmic side of the plasma 
membrane or the cytoplasmic side of the endoplasmic reticulum and the 


outer membrane of the nuclear envelope ( [link]). Electron microscopy has 
shown us that ribosomes, which are large complexes of protein and RNA, 
consist of two subunits, aptly called large and small ( [link]). Ribosomes 
receive their “orders” for protein synthesis from the nucleus where the 
DNA is transcribed into messenger RNA (mRNA). The mRNA travels to 
the ribosomes, which translate the code provided by the sequence of the 
nitrogenous bases in the mRNA into a specific order of amino acids ina 
protein. Amino acids are the building blocks of proteins. 


Growing peptide 
chain 


Ribosome 
large 
subunit 


tRNA 


Ribosome 
small 
subunit 


Ribosomes are made up of a large 
subunit (top) and a small subunit 
(bottom). During protein synthesis, 
ribosomes assemble amino acids into 
proteins. 


Because proteins synthesis is an essential function of all cells (including 
enzymes, hormones, antibodies, pigments, structural components, and 
surface receptors), ribosomes are found in practically every cell. Ribosomes 
are particularly abundant in cells that synthesize large amounts of protein. 
For example, the pancreas is responsible for creating several digestive 


enzymes and the cells that produce these enzymes contain many ribosomes. 
Thus, we see another example of form following function. 


Mitochondria 


Mitochondria (singular = mitochondrion) are often called the 
“powerhouses” or “energy factories” of a cell because they are responsible 
for making adenosine triphosphate (ATP), the cell’s main energy-carrying 
molecule. ATP represents the short-term stored energy of the cell. Cellular 
respiration is the process of making ATP using the chemical energy found 
in glucose and other nutrients. In mitochondria, this process uses oxygen 
and produces carbon dioxide as a waste product. In fact, the carbon dioxide 
that you exhale with every breath comes from the cellular reactions that 
produce carbon dioxide as a byproduct. 


In keeping with our theme of form following function, it is important to 
point out that muscle cells have a very high concentration of mitochondria 
that produce ATP. Your muscle cells need a lot of energy to keep your body 
moving. When your cells don’t get enough oxygen, they do not make a lot 
of ATP. Instead, the small amount of ATP they make in the absence of 
oxygen is accompanied by the production of lactic acid. 


Mitochondria are oval-shaped, double membrane organelles ( [link]) that 
have their own ribosomes and DNA. Each membrane is a phospholipid 
bilayer embedded with proteins. The inner layer has folds called cristae. 
The area surrounded by the folds is called the mitochondrial matrix. The 
cristae and the matrix have different roles in cellular respiration. 


Mitochondrial 
matrix 


Cristae 


Outer membrane 
Inner membrane 


This electron micrograph shows a 
mitochondrion as viewed with a 
transmission electron microscope. 
This organelle has an outer membrane 
and an inner membrane. The inner 
membrane contains folds, called 
cristae, which increase its surface 
area. The space between the two 
membranes is called the 
intermembrane space, and the space 
inside the inner membrane is called 
the mitochondrial matrix. ATP 
synthesis takes place on the inner 
membrane. (credit: modification of 
work by Matthew Britton; scale-bar 
data from Matt Russell) 


Peroxisomes 


Peroxisomes are small, round organelles enclosed by single membranes. 
They carry out oxidation reactions that break down fatty acids and amino 
acids. They also detoxify many poisons that may enter the body. (Many of 
these oxidation reactions release hydrogen peroxide, H»O>, which would be 
damaging to cells; however, when these reactions are confined to 
peroxisomes, enzymes safely break down the H»O> into oxygen and water.) 
For example, alcohol is detoxified by peroxisomes in liver cells. 
Glyoxysomes, which are specialized peroxisomes in plants, are responsible 
for converting stored fats into sugars. 


Vesicles and Endosomes 


Vesicles and endosomes are membrane-bound sacs that function in storage 
and transport. Other than the fact that vacuoles are somewhat larger than 
vesicles, there is a very subtle distinction between them: The membranes of 


vesicles can fuse with either the plasma membrane or other membrane 
systems within the cell. Additionally, some agents such as enzymes within 
plant vacuoles break down macromolecules. The membrane of a vacuole 
does not fuse with the membranes of other cellular components. 


Animal Cells versus Plant Cells 


At this point, you know that each eukaryotic cell has a plasma membrane, 
cytoplasm, a nucleus, ribosomes, mitochondria, peroxisomes, and in some, 
vacuoles, but there are some striking differences between animal and plant 
cells. While both animal and plant cells have microtubule organizing 
centers (MTOCs), animal cells also have centrioles associated with the 
MTOC: a complex called the centrosome. Animal cells each have a 
centrosome and lysosomes, whereas plant cells do not. Plant cells have a 
cell wall, chloroplasts and other specialized plastids, and a large central 
vacuole, whereas animal cells do not. 


The Centrosome 


The centrosome is a microtubule-organizing center found near the nuclei of 
animal cells. It contains a pair of centrioles, two structures that lie 
perpendicular to each other ( [link]). Each centriole is a cylinder of nine 
triplets of microtubules. 


Centriole 


Microtubule 
triplet 
Centriole 


The centrosome consists of two 
centrioles that lie at right angles to 
each other. Each centriole is a cylinder 
made up of nine triplets of 
microtubules. Nontubulin proteins 
(indicated by the green lines) hold the 
microtubule triplets together. 


The centrosome (the organelle where all microtubules originate) replicates 
itself before a cell divides, and the centrioles appear to have some role in 
pulling the duplicated chromosomes to opposite ends of the dividing cell. 
However, the exact function of the centrioles in cell division isn’t clear, 
because cells that have had the centrosome removed can still divide, and 
plant cells, which lack centrosomes, are capable of cell division. 


Lysosomes 


Another set of organelles only found in eukaryotes are lysosomes. The 
lysosomes are the cell’s “garbage disposal.” Enzymes within the lysosomes 
aid the breakdown of proteins, polysaccharides, lipids, nucleic acids, and 
even worn-out organelles. These enzymes are active at a much lower pH 
than that of the cytoplasm. Therefore, the pH within lysosomes is more 
acidic than the pH of the cytoplasm. Many reactions that take place in the 
cytoplasm could not occur at a low pH, so again, the advantage of 
compartmentalizing the eukaryotic cell into organelles is apparent. 


The Cell Wall 


If you examine [link]b, the diagram of a plant cell, you will see a structure 
external to the plasma membrane called the cell wall. The cell wall is a 
rigid covering that protects the cell, provides structural support, and gives 
shape to the cell. Fungal and protistan cells also have cell walls. While the 


chief component of prokaryotic cell walls is peptidoglycan, the major 
organic molecule in the plant cell wall is cellulose ( [link]), a 
polysaccharide made up of glucose units. Have you ever noticed that when 
you bite into a raw vegetable, like celery, it crunches? That’s because you 
are tearing the rigid cell walls of the celery cells with your teeth. 


H,C — OH H,C — OH 


OH H OH H OH H 
oO OH H OH H 


HC — OH H,C — OH H.C — OH 


Cellulose is a long chain of B-glucose 
molecules connected by a 1-4 linkage. 
The dashed lines at each end of the 
figure indicate a series of many more 
glucose units. The size of the page 
makes it impossible to portray an 
entire cellulose molecule. 


Chloroplasts 


Like the mitochondria, chloroplasts have their own DNA and ribosomes, 
but chloroplasts have an entirely different function. Chloroplasts are plant 
cell organelles that carry out photosynthesis. Photosynthesis is the series of 
reactions that use carbon dioxide, water, and light energy to make glucose 
and oxygen. This is a major difference between plants and animals; plants 
(autotrophs) are able to make their own food, like sugars, while animals 
(heterotrophs) must ingest their food. 


Like mitochondria, chloroplasts have outer and inner membranes, but 
within the space enclosed by a chloroplast’s inner membrane is a set of 
interconnected and stacked fluid-filled membrane sacs called thylakoids ( 


[link]). Each stack of thylakoids is called a granum (plural = grana). The 
fluid enclosed by the inner membrane that surrounds the grana is called the 
stroma. 


Outer Intermembrane Inner Stroma 
membrane space membrane (aqueous fluid) 


Thylakoid 


Granum 
(stack of thylakoids) 


The chloroplast has an outer 
membrane, an inner membrane, and 
membrane structures called thylakoids 
that are stacked into grana. The space 
inside the thylakoid membranes is 
called the thylakoid space. The light 
harvesting reactions take place in the 
thylakoid membranes, and the 
synthesis of sugar takes place in the 
fluid inside the inner membrane, 
which is called the stroma. 
Chloroplasts also have their own 
genome, which is contained on a 
single circular chromosome. 


The chloroplasts contain a green pigment called chlorophyll, which 
captures the light energy that drives the reactions of photosynthesis. Like 
plant cells, photosynthetic protists also have chloroplasts. Some bacteria 
perform photosynthesis, but their chlorophyll is not relegated to an 
organelle. 


The Central Vacuole 


Previously, we mentioned vacuoles as essential components of plant cells. 
If you look at [link]b, you will see that plant cells each have a large central 
vacuole that occupies most of the area of the cell. The central vacuole 
plays a key role in regulating the cell’s concentration of water in changing 
environmental conditions. Have you ever noticed that if you forget to water 
a plant for a few days, it wilts? That’s because as the water concentration in 
the soil becomes lower than the water concentration in the plant, water 
moves out of the central vacuoles and cytoplasm. As the central vacuole 
shrinks, it leaves the cell wall unsupported. This loss of support to the cell 
walls of plant cells results in the wilted appearance of the plant. 


The central vacuole also supports the expansion of the cell. When the 
central vacuole holds more water, the cell gets larger without having to 
invest a lot of energy in synthesizing new cytoplasm. 


Protists 


Introduction 

"The 31th of May, I perceived in the same water more of those Animals, as 
also some that were somewhat bigger. And I imagine that ten hundred 
thousand of these little Creatures do not equal an ordinary grain of Sand in 
bigness..." Antoni von Leeuwenhoek, Letter to H. Oldenburg, 9 October 
1676 


Von Leeuwenhoek's amazement at seeing protists for the first time is 
understandable. These tiny creatures are abundant, diverse, and fit into 
many biological niches. There are over 100,000 described living species of 
protists, and it is unclear how many undescribed species may exist. Since 
many protists live as commensals or parasites in other organisms and these 
relationships are often species-specific, there is a huge potential for protist 
diversity that matches the diversity of hosts. As the catchall term for 
eukaryotic organisms that are not animal, plant, or fungi, it is not surprising 
that very few characteristics are common to all protists. Since Protista is a 
catchall group of organisms, Biologists are now investigating the 
evolutionary relationships of this groups and are formulating many new 
Kingdoms within the group of Protists. 


Cell Structure 


The cells of protists are among the most elaborate of all cells. Most protists 
are microscopic and unicellular, but some true multicellular forms exist. A 
few protists live as colonies that behave in some ways as a group of free- 
living cells and in other ways as a multicellular organism. Still other protists 
are composed of enormous, multinucleate, single cells that look like 
amorphous blobs of slime, or in other cases, like ferns. In fact, many protist 
cells are multinucleated; in some species, the nuclei are different sizes and 
have distinct roles in protist cell function. 


Single protist cells range in size from less than a micrometer to three meters 
in length to hectares. Protist cells may be enveloped by animal-like plasma 
membranes or plant-like cell walls. Others are encased in glassy silica- 
based shells or wound with pellicles of interlocking protein strips. The 


pellicle functions like a flexible coat of armor, preventing the protist from 
being torn or pierced without compromising its range of motion. 


Metabolism 


Protists exhibit many forms of nutrition and may be aerobic or anaerobic. 
Protists that store energy by photosynthesis belong to a group of 
photoautotrophs and are characterized by the presence of chloroplasts. 
Other protists are heterotrophic and consume organic materials (such as 
other organisms) to obtain nutrition. Amoebas and some other heterotrophic 
protist species ingest particles by a process called phagocytosis, in which 
the plasma membrane engulfs a food particle and brings it inward, pinching 
off an intracellular membranous sac, or vesicle, called a food vacuole 
({link]). The vesicle containing the ingested particle, the phagosome, then 
fuses with a lysosome containing hydrolytic enzymes to produce a 
phagolysosome, and the food particle is broken down into small molecules 
that can diffuse into the cytoplasm and be used in cellular metabolism. 
Undigested remains ultimately are expelled from the cell via exocytosis. 


Phagocytosis 


Food particle | Food vacuole Exocytic vesicle containing 
undigested material 


Pseudopods 


Lysosome containing ~ 
digestive enzymes 


The stages of phagocytosis 
include the engulfment of a 
food particle, the digestion of 
the particle using hydrolytic 
enzymes contained within a 


lysosome, and the expulsion of 
undigested materials from the 
cell. 


Subtypes of heterotrophs, called saprobes, absorb nutrients from dead 
organisms or their organic wastes. Some protists can function as 
mixotrophs, obtaining nutrition by photoautotrophic or heterotrophic 
routes, depending on whether sunlight or organic nutrients are available. 


Motility 


The majority of protists are motile, but different types of protists have 
evolved varied modes of movement ([link]). Some protists have one or 
more flagella, which they rotate or whip. Others are covered in rows or tufts 
of tiny cilia that they coordinately beat to swim. Still others form 
cytoplasmic extensions called pseudopodia anywhere on the cell, anchor the 
pseudopodia to a substrate, and pull themselves forward. Some protists can 
move toward or away from a stimulus, a movement referred to as taxis. 
Movement toward light, termed phototaxis, is accomplished by coupling 
their locomotion strategy with a light-sensing organ. 


Paramecium Amoeba Euglena 


Pseudopod Flagellum 


(a) (b) (c) 


Protists use various methods for transportation. (a) 
Paramecium waves hair-like appendages called cilia to 
propel itself. (b) Amoeba uses lobe-like pseudopodia to 


anchor itself to a solid surface and pull itself forward. (c) 
Euglena uses a whip-like tail called a flagellum to propel 
itself. 


Life Cycles 


Protists reproduce by a variety of mechanisms. Most undergo some form of 
asexual reproduction, such as binary fission, to produce two daughter cells. 
In protists, binary fission can be divided into transverse or longitudinal, 
depending on the axis of orientation; sometimes Paramecium exhibits this 
method. Some protists such as the true slime molds exhibit multiple fission 
and simultaneously divide into many daughter cells. Others produce tiny 
buds that go on to divide and grow to the size of the parental protist. Sexual 
reproduction, involving meiosis and fertilization, is common among 
protists, and many protist species can switch from asexual to sexual 
reproduction when necessary. Sexual reproduction is often associated with 
periods when nutrients are depleted or environmental changes occur. Sexual 
reproduction may allow the protist to recombine genes and produce new 
variations of progeny that may be better suited to surviving in the new 
environment. However, sexual reproduction is often associated with 
resistant cysts that are a protective, resting stage. Depending on their 
habitat, the cysts may be particularly resistant to temperature extremes, 
desiccation, or low pH. This strategy also allows certain protists to “wait 
out” stressors until their environment becomes more favorable for survival 
or until they are carried (such as by wind, water, or transport on a larger 
organism) to a different environment, because cysts exhibit virtually no 
cellular metabolism. 


Protist life cycles range from simple to extremely elaborate. Certain 
parasitic protists have complicated life cycles and must infect different host 
species at different developmental stages to complete their life cycle. Some 
protists are unicellular in the haploid form and multicellular in the diploid 
form, a strategy employed by animals. Other protists have multicellular 
stages in both haploid and diploid forms, a strategy called alternation of 
generations that is also used by plants. 


Habitats 


Nearly all protists exist in some type of aquatic environment, including 
freshwater and marine environments, damp soil, and even snow. Several 
protist species are parasites that infect animals or plants. A few protist 
species live on dead organisms or their wastes, and contribute to their 
decay. 


Fungi 


Introduction 

"When brewer's yeast is mixed with water the microscope reveals that the 
yeast dissolves into endless small balls, which are scarcely 1/800th of a line 
in diameter... If these small balls are placed in sugar water, it can be seen 
that they consist of the eggs of animals. As they expand, they burst, and 
from them develop small creatures that multiply with unbelievable rapidity 
in a most unheard-of way." Friedrich Wohler, Annalen der Pharmacie und 
Chemie, 29:100-104, 1839 


WoOhler's fanciful depiction of yeast as tiny animals, while not reflecting 
current taxonomic opinions, is understandable. Yeast, a single-celled 
member of the Kingdom Fungi, share many characteristics with animals, 
include being heterotrophic. But they also have cell walls, a characteristic 
that they share with plants. But even though a superficial glance might 
indicate that Fungi occupy the middle ground between animals and plants, 
they are unique in several ways, and have many interesting and useful 
metabolites and products (such as penicillin, or ethanol). So let's briefly 
introduce the Fungi here, and return to them in a later module for a more 
detailed look at these mysterious creatures. 


(a) (b) (c) 


The (a) familiar mushroom is only one type of fungus. The 
brightly colored fruiting bodies of this (b) coral fungus are 
displayed. This (c) electron micrograph shows the spore- 
bearing structures of Aspergillus, a type of toxic fungi 
found mostly in soil and plants. (credit a: modification of 


work by Chris Wee; credit b: modification of work by Cory 
Zanker; credit c: modification of work by Janice Haney 
Carr, Robert Simmons, CDC; scale-bar data from Matt 
Russell) 


The word fungus comes from the Latin word for mushroom. Indeed, the 
familiar mushrooms are fungi, but there are many other types of fungi as 
well ((link]). The kingdom Fungi includes an enormous variety of living 
organisms collectively referred to as Eumycota, or true fungi. While 
scientists have identified about 100,000 species of fungi, this is only a 
fraction of the over 1 million species likely present on Earth. Edible 
mushrooms, yeasts, black mold, and Penicillium notatum (the producer of 
the antibiotic penicillin) are all members of the kingdom Fungi, which 
belongs to the domain Eukarya. As eukaryotes, a typical fungal cell 
contains a true nucleus and many membrane-bound organelles. 


Fungi were once considered plant-like organisms; however, DNA 
comparisons have shown that fungi are more closely related to animals than 
plants. Fungi are not capable of photosynthesis: They use complex organic 
compounds as sources of energy and carbon. Some fungal organisms 
multiply only asexually, whereas others undergo both asexual reproduction 
and sexual reproduction. Most fungi produce a large number of spores that 
are disseminated by the wind. Like bacteria, fungi play an essential role in 
ecosystems, because they are decomposers and participate in the cycling of 
nutrients by breaking down organic materials into simple molecules. 


Fungi often interact with other organisms, forming mutually beneficial or 
mutualistic associations. Fungi also cause serious infections in plants and 
animals. For example, Dutch elm disease is a particularly devastating 
fungal infection that destroys many native species of elm (Ulmus spp.). The 
fungus infects the vascular system of the tree. It was accidentally 
introduced to North America in the 1900s and decimated elm trees across 
the continent. Dutch elm disease is caused by the fungus Ophiostoma ulmi. 
The elm bark beetle acts as a vector and transmits the disease from tree to 


tree. Many European and Asiatic elms are less susceptible than American 
elms. 


In humans, fungal infections are generally considered challenging to treat 
because, unlike bacteria, they do not respond to traditional antibiotic 
therapy since they are also eukaryotes. These infections may prove deadly 
for individuals with a compromised immune system. 


Fungi have many commercial applications. The food industry uses yeasts in 
baking, brewing, and wine making. Many industrial compounds are 
byproducts of fungal fermentation. Fungi are the source of many 
commercial enzymes and antibiotics. 


Cell Structure and Function 


Fungi are eukaryotes and as such have a complex cellular organization 
({link]). As eukaryotes, fungal cells contain a membrane-bound nucleus. A 
few types of fungi have structures comparable to the plasmids (loops of 
DNA) seen in bacteria. Fungal cells also contain mitochondria and a 
complex system of internal membranes, including the endoplasmic 
reticulum and Golgi apparatus. 


Fungal cells do not have chloroplasts. Although the photosynthetic pigment 
chlorophyll is absent, many fungi display bright colors, ranging from red to 
green to black. The poisonous Amanita muscaria (fly agaric) is 
recognizable by its bright red cap with white patches. Other fungi can be 
red, or purple, or blue, although many are simply white or brownish. 
Pigments in fungi are associated with the cell wall and play a protective role 
against ultraviolet radiation. Some pigments are toxic. 


A. Fungal Hyphae B. Cellular components of 
a fungal hypha 


Fungal Hyphae. A - Diagram of a branching hyphal mass. B - Diagram 
of the cellular components of the tip of one of the hyphae. 1- Cell wall 
2- Septum 3- Mitochondrion 4- Vacuole 5- Ergosterol crystal 6- 
Ribosome 7- Nucleus 8- Endoplasmic reticulum 9- Lipid body 10- 
Plasma membrane 11- Growth tip and vesicles 12- Golgi apparatus. 
(From Creative Commons, original artist - AHiggins12) 


Like plant cells, fungal cells are surrounded by a thick cell wall; however, 
the rigid layers contain the complex polysaccharides chitin and glucan. 
Cellulose, the main component of plant cell walls, is found rarely in fungi. 
Chitin, also found in the exoskeleton of insects, gives structural strength to 
the cell walls of fungi. The cell wall protects the cell from desiccation and 
predators. Fungi have plasma membranes similar to other eukaryotes, 
except that the structure is stabilized by ergosterol, a steroid molecule that 
functions like the cholesterol found in animal plasma membranes. Most 
members of the kingdom Fungi are nonmotile. Flagella are produced only 
by the gametes in the primitive division Chytridiomycota. 


Eukaryotic Origins 


Introduction 

"In most of the animals we think we know best (mammals, reptiles, 
insects), the genomes that determine limbs, eyes, and nervous systems, for 
example, are very similar to our own. These animals, like us, are doubly 
genomic. Even some unicellular beings that do not have eyes, limbs, or 
nervous systems--such as amoebas and paramecia--contain both nuclear and 
mitochondrial genomes. Plants and algae have these double genomes as 
well, plus a third genome, of symbiotic origin. During their evolutionary 
history, they ingested (but did not digest) photosynthetic blue-green 
bacteria. Therefore, all visible photosynthetic organisms have at least three 
genomes. But many organisms--such as the protists that inhabit termites-- 
contain within them up to five or more genomes." Lynn Margulis and 
Dorion Sagan, "The Beast with Five Genomes", Natural History Vol. 110 
Issue 5, p. 38, 2001 


Living things fall into three large groups: Archaea, Bacteria, and Eukarya. 
The first two have prokaryotic cells, and the third contains all eukaryotes. 
But, as noted above, eukaryotes contain multiple genomes, and those 
genomes indicate that eukaryotes probably arose by when one ancestor 
"captured" another. A relatively sparse fossil record is available to help 
discern what the first members of each of these lineages looked like, so it is 
possible that all the events that led to the last common ancestor of extant 
eukaryotes will never be clarified by the fossil record. However, 
comparative biology of extant organisms, genomic analysis, and the limited 
fossil record provide some insight into the history of Eukarya. 


The earliest fossils found appear to be Bacteria, most likely cyanobacteria. 
They are about 3.5 billion years old and are recognizable because of their 
relatively complex structure and, for prokaryotes, relatively large cells. 
Most other prokaryotes have small cells, 1 or 2 ym in size, and would be 
difficult to pick out as fossils. Most living eukaryotes have cells measuring 
10 pm or greater. Structures this size, which might be fossils, appear in the 
geological record about 2.1 billion years ago. 


Characteristics of Eukaryotes 


Data from these fossils have led comparative biologists to the conclusion 
that living eukaryotes are all descendants of a single common ancestor. 
Mapping the characteristics found in all major groups of eukaryotes reveals 
that the following characteristics must have been present in the last 
common ancestor, because these characteristics are present in at least some 
of the members of each major lineage. 


iL, 


Cells with nuclei surrounded by a nuclear envelope with nuclear pores. 
This is the single characteristic that is both necessary and sufficient to 
define an organism as a eukaryote. All extant eukaryotes have cells 
with nuclei. 


. Mitochondria. Some extant eukaryotes have very reduced remnants of 


mitochondria in their cells, whereas other members of their lineages 
have “typical” mitochondria. 


. A cytoskeleton containing the structural and motility components 


called actin microfilaments and microtubules. All extant eukaryotes 
have these cytoskeletal elements. 


. Flagella and cilia, organelles associated with cell motility. Some extant 


eukaryotes lack flagella and/or cilia, but they are descended from 
ancestors that possessed them. 


. Chromosomes, each consisting of a linear DNA molecule coiled 


around basic (alkaline) proteins called histones. The few eukaryotes 
with chromosomes lacking histones clearly evolved from ancestors 
that had them. 


. Mitosis, a process of nuclear division wherein replicated chromosomes 


are divided and separated using elements of the cytoskeleton. Mitosis 
is universally present in eukaryotes. 


. Sex, a process of genetic recombination unique to eukaryotes in which 


diploid nuclei at one stage of the life cycle undergo meiosis to yield 
haploid nuclei and subsequent karyogamy, a stage where two haploid 
nuclei fuse together to create a diploid zygote nucleus. 


. Members of all major lineages have cell walls, and it might be 


reasonable to conclude that the last common ancestor could make cell 
walls during some stage of its life cycle. However, not enough is 
known about eukaryotes’ cell walls and their development to know 
how much homology exists among them. If the last common ancestor 


could make cell walls, it is clear that this ability must have been lost in 
many groups. 


Endosymbiosis and the Evolution of Eukaryotes 


In order to understand eukaryotic organisms fully, it is necessary to 
understand that all extant eukaryotes are descendants of a chimeric 
organism that was a composite of a host cell and the cell(s) of an alpha- 
proteobacterium that “took up residence” inside it. This major theme in the 
origin of eukaryotes is known as endosymbiosis, one cell engulfing another 
such that the engulfed cell survives and both cells benefit. Over many 
generations, a symbiotic relationship can result in two organisms that 
depend on each other so completely that neither could survive on its own. 
Endosymbiotic events likely contributed to the origin of the last common 
ancestor of today’s eukaryotes and to later diversification in certain lineages 
of eukaryotes ({link]). Before explaining this further, it is necessary to 
consider metabolism in prokaryotes. 


Prokaryotic Metabolism 


Many important metabolic processes arose in prokaryotes, and some of 
these, such as nitrogen fixation, are never found in eukaryotes. The process 
of aerobic respiration is found in all major lineages of eukaryotes, and it is 
localized in the mitochondria. Aerobic respiration is also found in many 
lineages of prokaryotes, but it is not present in all of them, and many forms 
of evidence suggest that such anaerobic prokaryotes never carried out 
aerobic respiration nor did their ancestors. 


While today’s atmosphere is about one-fifth molecular oxygen (O>), 
geological evidence shows that it originally lacked Oy. Without oxygen, 
aerobic respiration would not be expected, and living things would have 
relied on fermentation instead. At some point before, about 3.5 billion years 
ago, some prokaryotes began using energy from sunlight to power anabolic 
processes that reduce carbon dioxide to form organic compounds. That is, 
they evolved the ability to photosynthesize. Hydrogen, derived from various 


sources, was captured using light-powered reactions to reduce fixed carbon 
dioxide in the Calvin cycle. The group of Gram-negative bacteria that gave 
rise to cyanobacteria used water as the hydrogen source and released O» as 
a waste product. 


Eventually, the amount of photosynthetic oxygen built up in some 
environments to levels that posed a risk to living organisms, since it can 
damage many organic compounds. Various metabolic processes evolved 
that protected organisms from oxygen, one of which, aerobic respiration, 
also generated high levels of ATP. It became widely present among 
prokaryotes, including in a group we now call alpha-proteobacteria. 
Organisms that did not acquire aerobic respiration had to remain in oxygen- 
free environments. Originally, oxygen-rich environments were likely 
localized around places where cyanobacteria were active, but by about 2 
billion years ago, geological evidence shows that oxygen was building up to 
higher concentrations in the atmosphere. Oxygen levels similar to today’s 
levels only arose within the last 700 million years. 


Recall that the first fossils that we believe to be eukaryotes date to about 2 
billion years old, so they appeared as oxygen levels were increasing. Also, 
recall that all extant eukaryotes descended from an ancestor with 
mitochondria. These organelles were first observed by light microscopists 
in the late 1800s, where they appeared to be somewhat worm-shaped 
structures that seemed to be moving around in the cell. Some early 
observers suggested that they might be bacteria living inside host cells, but 
these hypotheses remained unknown or rejected in most scientific 
communities. 


Endosymbiotic Theory 


As cell biology developed in the twentieth century, it became clear that 
mitochondria were the organelles responsible for producing ATP using 
aerobic respiration. In the 1960s, American biologist Lynn Margulis 
developed endosymbiotic theory, which states that eukaryotes may have 
been a product of one cell engulfing another, one living within another, and 
evolving over time until the separate cells were no longer recognizable as 


such. In 1967, Margulis introduced new work on the theory and 
substantiated her findings through microbiological evidence. Although 
Margulis’ work initially was met with resistance, this once-revolutionary 
hypothesis is now widely accepted, with work progressing on uncovering 
the steps involved in this evolutionary process and the key players involved. 
Much still remains to be discovered about the origins of the cells that now 
make up the cells in all living eukaryotes. 


Broadly, it has become clear that many of our nuclear genes and the 
molecular machinery responsible for replication and expression appear 
closely related to those in Archaea. On the other hand, the metabolic 
organelles and genes responsible for many energy-harvesting processes had 
their origins in bacteria. Much remains to be clarified about how this 
relationship occurred; this continues to be an exciting field of discovery in 
biology. For instance, it is not known whether the endosymbiotic event that 
led to mitochondria occurred before or after the host cell had a nucleus. 
Such organisms would be among the extinct precursors of the last common 
ancestor of eukaryotes. 


Mitochondria 


One of the major features distinguishing prokaryotes from eukaryotes is the 
presence of mitochondria. Eukaryotic cells may contain anywhere from 
one to several thousand mitochondria, depending on the cell’s level of 
energy consumption. Each mitochondrion measures 1 to 10 or greater 
micrometers in length and exists in the cell as an organelle that can be ovoid 
to worm-shaped to intricately branched ({link]). Mitochondria arise from 
the division of existing mitochondria; they may fuse together; and they may 
be moved around inside the cell by interactions with the cytoskeleton. 
However, mitochondria cannot survive outside the cell. As the atmosphere 
was oxygenated by photosynthesis, and as successful aerobic prokaryotes 
evolved, evidence suggests that an ancestral cell with some membrane 
compartmentalization engulfed a free-living aerobic prokaryote, specifically 
an alpha-proteobacterium, thereby giving the host cell the ability to use 
oxygen to release energy stored in nutrients. Alpha-proteobacteria are a 
large group of bacteria that includes species symbiotic with plants, disease 


organisms that can infect humans via ticks, and many free-living species 
that use light for energy. Several lines of evidence support that 
mitochondria are derived from this endosymbiotic event. Most 
mitochondria are shaped like alpha-proteobacteria and are surrounded by 
two membranes, which would result when one membrane-bound organism 
was engulfed into a vacuole by another membrane-bound organism. The 
mitochondrial inner membrane is extensive and involves substantial 
infoldings called cristae that resemble the textured, outer surface of alpha- 
proteobacteria. The matrix and inner membrane are rich with the enzymes 
necessary for aerobic respiration. 


In this transmission electron 


micrograph of mitochondria in a 
mammalian lung cell, the 
cristae, infoldings of the 
mitochondrial inner membrane, 
can be seen in cross-section. 
(credit: Louise Howard) 


Mitochondria divide independently by a process that resembles binary 
fission in prokaryotes. Specifically, mitochondria are not formed from 
scratch (de novo) by the eukaryotic cell; they reproduce within it and are 
distributed with the cytoplasm when a cell divides or two cells fuse. 


Therefore, although these organelles are highly integrated into the 
eukaryotic cell, they still reproduce as if they are independent organisms 
within the cell. However, their reproduction is synchronized with the 
activity and division of the cell. Mitochondria have their own (usually) 
circular DNA chromosome that is stabilized by attachments to the inner 
membrane and carries genes similar to genes expressed by alpha- 
proteobacteria. Mitochondria also have special ribosomes and transfer 
RNAs that resemble these components in prokaryotes. These features all 
support that mitochondria were once free-living prokaryotes. 


Mitochondria that carry out aerobic respiration have their own genomes, 
with genes similar to those in alpha-proteobacteria. However, many of the 
genes for respiratory proteins are located in the nucleus. When these genes 
are compared to those of other organisms, they appear to be of alpha- 
proteobacterial origin. Additionally, in some eukaryotic groups, such genes 
are found in the mitochondria, whereas in other groups, they are found in 
the nucleus. This has been interpreted as evidence that genes have been 
transferred from the endosymbiont chromosome to the host genome. This 
loss of genes by the endosymbiont is probably one explanation why 
mitochondria cannot live without a host. 


Some living eukaryotes are anaerobic and cannot survive in the presence of 
too much oxygen. Some appear to lack organelles that could be recognized 
as mitochondria. In the 1970s to the early 1990s, many biologists suggested 
that some of these eukaryotes were descended from ancestors whose 
lineages had diverged from the lineage of mitochondrion-containing 
eukaryotes before endosymbiosis occurred. However, later findings suggest 
that reduced organelles are found in most, if not all, anaerobic eukaryotes, 
and that all eukaryotes appear to carry some genes in their nuclei that are of 
mitochondrial origin. In addition to the aerobic generation of ATP, 
mitochondria have several other metabolic functions. One of these 
functions is to generate clusters of iron and sulfur that are important 
cofactors of many enzymes. Such functions are often associated with the 
reduced mitochondrion-derived organelles of anaerobic eukaryotes. 
Therefore, most biologists accept that the last common ancestor of 
eukaryotes had mitochondria. 


Plastids 


Some groups of eukaryotes are photosynthetic. Their cells contain, in 
addition to the standard eukaryotic organelles, another kind of organelle 
called a plastid. When such cells are carrying out photosynthesis, their 
plastids are rich in the pigment chlorophyll a and a range of other pigments, 
called accessory pigments, which are involved in harvesting energy from 
light. Photosynthetic plastids are called chloroplasts ([link]). 


(a) (b) 


(a) This chloroplast cross-section illustrates its elaborate 
inner membrane organization. Stacks of thylakoid 
membranes compartmentalize photosynthetic enzymes and 
provide scaffolding for chloroplast DNA. (b) In this 
micrograph of Elodea sp., the chloroplasts can be seen as 
small green spheres. (credit b: modification of work by 
Brandon Zierer; scale-bar data from Matt Russell) 


Like mitochondria, plastids appear to have an endosymbiotic origin. This 
hypothesis was also championed by Lynn Margulis. Plastids are derived 
from cyanobacteria that lived inside the cells of an ancestral, aerobic, 
heterotrophic eukaryote. This is called primary endosymbiosis, and plastids 
of primary origin are surrounded by two membranes. The best evidence is 
that this has happened twice in the history of eukaryotes. In one case, the 
common ancestor of the major lineage/supergroup Archaeplastida took on a 


cyanobacterial endosymbiont; in the other, the ancestor of the small 
amoeboid rhizarian taxon, Paulinella, took on a different cyanobacterial 
endosymbiont. Almost all photosynthetic eukaryotes are descended from 
the first event, and only a couple of species are derived from the other. 


Cyanobacteria are a group of Gram-negative bacteria with all the 
conventional structures of the group. However, unlike most prokaryotes, 
they have extensive, internal membrane-bound sacs called thylakoids. 
Chlorophyll is a component of these membranes, as are many of the 
proteins of the light reactions of photosynthesis. Cyanobacteria also have 
the peptidoglycan wall and lipopolysaccharide layer associated with Gram- 
negative bacteria. 


Chloroplasts of primary origin have thylakoids, a circular DNA 
chromosome, and ribosomes similar to those of cyanobacteria. Each 
chloroplast is surrounded by two membranes. In the group of 
Archaeplastida called the glaucophytes and in Paulinella, a thin 
peptidoglycan layer is present between the outer and inner plastid 
membranes. All other plastids lack this relictual cyanobacterial wall. The 
outer membrane surrounding the plastid is thought to be derived from the 
vacuole in the host, and the inner membrane is thought to be derived from 
the plasma membrane of the symbiont. 


There is also, as with the case of mitochondria, strong evidence that many 
of the genes of the endosymbiont were transferred to the nucleus. Plastids, 
like mitochondria, cannot live independently outside the host. In addition, 
like mitochondria, plastids are derived from the division of other plastids 
and never built from scratch. Researchers have suggested that the 
endosymbiotic event that led to Archaeplastida occurred 1 to 1.5 billion 
years ago, at least 5 hundred million years after the fossil record suggests 
that eukaryotes were present. 


Not all plastids in eukaryotes are derived directly from primary 
endosymbiosis. Some of the major groups of algae became photosynthetic 
by secondary endosymbiosis, that is, by taking in either green algae or red 
algae (both from Archaeplastida) as endosymbionts ([link]ab). Numerous 
microscopic and genetic studies have supported this conclusion. Secondary 
plastids are surrounded by three or more membranes, and some secondary 


plastids even have clear remnants of the nucleus of endosymbiotic alga. 
Others have not “kept” any remnants. There are cases where tertiary or 
higher-order endosymbiotic events are the best explanations for plastids in 
some eukaryotes. 


(b) 


(a) Red algae and (b) green algae (visualized by light 
microscopy) share similar DNA sequences with 
photosynthetic cyanobacteria. Scientists speculate 
that, in a process called endosymbiosis, an ancestral 
prokaryote engulfed a photosynthetic cyanobacterium 
that evolved into modern-day chloroplasts. (credit a: 
modification of work by Ed Bierman; credit b: 
modification of work by G. Fahnenstiel, NOAA; 
scale-bar data from Matt Russell) 


The ENDOSYMBIOTIC THEORY 


@ Infoldings in the plasma In a second endosymbiotic 
membrane of an ancestral event, the early eukaryote 
prokaryote gave rise to consumed photosynthetic 
endomembrane components, bacteria that evolved into 
including a nucleus and chloroplasts. 


endoplasmic reticulum. 


Endoplasmic 


Nucleus : 
reticulum 


e\ 


Modern photosynthetic 
eukaryote 


Photosynthetic 
bacterium 


Proto-eukaryote 


In a first endosymbiotic event, Aerobic Mitochondrion 


the ancestral eukaryote bacterium 
consumed aerobic bacteria 
that evolved into mitochondria. 


Modern heterotrophic eukaryote 


The first eukaryote may have originated from an ancestral 
prokaryote that had undergone membrane proliferation, 
compartmentalization of cellular function (into a nucleus, 
lysosomes, and an endoplasmic reticulum), and the 
establishment of endosymbiotic relationships with an 
aerobic prokaryote, and, in some cases, a photosynthetic 
prokaryote, to form mitochondria and chloroplasts, 
respectively. 


Note: 

Evolution Connection 

Secondary Endosymbiosis in Chlorarachniophytes 

Endosymbiosis involves one cell engulfing another to produce, over time, a 
coevolved relationship in which neither cell could survive alone. The 
chloroplasts of red and green algae, for instance, are derived from the 
engulfment of a photosynthetic cyanobacterium by an early prokaryote. 
This leads to the question of the possibility of a cell containing an 
endosymbiont to itself become engulfed, resulting in a secondary 
endosymbiosis. Molecular and morphological evidence suggest that the 
chlorarachniophyte protists are derived from a secondary endosymbiotic 
event. Chlorarachniophytes are rare algae indigenous to tropical seas and 


sand that can be classified into the rhizarian supergroup. 
Chlorarachniophytes extend thin cytoplasmic strands, interconnecting 
themselves with other chlorarachniophytes, in a cytoplasmic network. 
These protists are thought to have originated when a eukaryote engulfed a 
green alga, the latter of which had already established an endosymbiotic 
relationship with a photosynthetic cyanobacterium ((link]). 


ra Vestigial nucleus __Plastid 
Primary Secondary 
endossrblods endosymbiosis 
One of the three 
H hi membranes 
eterotrophic surrounding the 
eukaryote 


plastid is lost. 


The hypothesized process of endosymbiotic 
events leading to the evolution of 
chlorarachniophytes is shown. In a primary 
endosymbiotic event, a heterotrophic 
eukaryote consumed a cyanobacterium. In a 
secondary endosymbiotic event, the cell 
resulting from primary endosymbiosis was 
consumed by a second cell. The resulting 
organelle became a plastid in modern 
chlorarachniophytes. 


Several lines of evidence support that chlorarachniophytes evolved from 
secondary endosymbiosis. The chloroplasts contained within the green 
algal endosymbionts still are capable of photosynthesis, making 
chlorarachniophytes photosynthetic. The green algal endosymbiont also 
exhibits a stunted vestigial nucleus. In fact, it appears that 
chlorarachniophytes are the products of an evolutionarily recent secondary 
endosymbiotic event. The plastids of chlorarachniophytes are surrounded 
by four membranes: The first two correspond to the inner and outer 
membranes of the photosynthetic cyanobacterium, the third corresponds to 
the green alga, and the fourth corresponds to the vacuole that surrounded 
the green alga when it was engulfed by the chlorarachniophyte ancestor. In 
other lineages that involved secondary endosymbiosis, only three 


membranes can be identified around plastids. This is currently rectified as 
a sequential loss of a membrane during the course of evolution. 

The process of secondary endosymbiosis is not unique to 
chlorarachniophytes. In fact, secondary endosymbiosis of green algae also 
led to euglenid protists, whereas secondary endosymbiosis of red algae led 
to the evolution of dinoflagellates, apicomplexans, and stramenopiles. 


Atoms, Isotopes, Ions, and Molecules: The Building Blocks 


""Through the discovery of Buchner, Biology was relieved of another 
fragment of mysticism. The splitting up of sugar into CO> and alcohol is no 
more the effect of a 'vital principle’ than the splitting up of cane sugar by 
invertase. The history of this problem is instructive, as it warns us against 
considering problems as beyond our reach because they have not yet found 
their solution."" Jacques Loeb, in The Dynamics of Living Matter, (1906) 


Loeb is referring to the Nobel Prize-winning experiments of Eduard 
Buchner, who proved that cells are not necessary for cellular chemical 
reactions to take place. This was one of the crucial steps toward the 
synthesis of biology and chemistry that culminates in the modern-day 
discipline we call biochemistry. The properties of matter are important in 
the study of biochemistry (and biology), so we need to introduce some 
chemical concepts to help us with that understanding. At its most 
fundamental level, life is made up of matter. Matter is any substance that 
occupies space and has mass. Elements are unique forms of matter with 
specific chemical and physical properties that cannot be broken down into 
smaller substances by ordinary chemical reactions. There are 118 elements, 
but only 92 occur naturally. The remaining elements have only been 
synthesized in laboratories, and are unstable. 


Each element is designated by its chemical symbol, which is a single 
capital letter or, when the first letter is already “taken” by another element, 
a combination of two letters. Some elements follow the English term for the 
element, such as C for carbon and Ca for calcium. Other elements’ 
chemical symbols derive from their Latin names; for example, the symbol 
for sodium is Na, referring to natrium, the Latin word for sodium. 


The four most abundant elements in all living organisms are oxygen (O), 
carbon (C), hydrogen (H), and nitrogen (N). In the non-living world, 
elements are found in different proportions, and some elements common to 
living organisms are relatively rare on the earth as a whole, as shown in 
[link]. For example, the atmosphere is rich in nitrogen and oxygen but 
contains little carbon and hydrogen, while the earth’s crust, although it 
contains oxygen and a small amount of hydrogen, has little nitrogen and 
carbon. In spite of their differences in abundance, all elements and the 


chemical reactions between them obey the same chemical and physical laws 
regardless of whether they are a part of the living or non-living world. 


Approximate Percentage of Elements in Living Organisms 
(Humans) Compared to the Non-living World 


Organisms Earth’s 
Element (Humans) Atmosphere Crust 
oo 65% 21% 46% 
Carbon (C) 18% trace trace 
Hydrogen ” “ 
(H) 10% trace 0.1% 
Nitrogen ji ) 
(N) 3% 78% trace 


The Structure of the Atom 


To understand how elements come together, we must first discuss the 
smallest component or building block of an element, the atom. An atom is 
the smallest unit of matter that retains all of the chemical properties of an 
element. For example, one gold atom has all of the properties of gold in that 
it is a solid metal at room temperature. A gold coin is simply a very large 
number of gold atoms molded into the shape of a coin and containing small 
amounts of other elements known as impurities. Gold atoms cannot be 
broken down into anything smaller while still retaining the properties of 
gold. 


An atom is composed of two regions: the nucleus, which is in the center of 
the atom and contains protons and neutrons, and the outermost region of 
the atom which holds its electrons in orbit around the nucleus, as illustrated 
in [link]. Atoms contain protons, electrons, and neutrons. The only 
exception is hydrogen (H), which is made of one proton and one electron, 
with no neutrons. 


Electrons 


Elements, such as helium, 
depicted here, are made up of 
atoms. Atoms are made up of 
protons and neutrons located 

within the nucleus, with electrons 
in orbitals surrounding the 
nucleus. 


Protons and neutrons have approximately the same mass, about 1.67 x 1074 
grams. Scientists arbitrarily define this amount of mass as one atomic mass 
unit (amu) or one Dalton, as shown in [link]. Although similar in mass, 
protons and neutrons differ in their electric charge. A proton is positively 
charged whereas a neutron is uncharged. Therefore, the number of 
neutrons in an atom contributes significantly to its mass, but not to its 
charge. Electrons are much smaller in mass than protons, weighing only 
9.11 x 10°°8 grams, or about 1/1800 of an atomic mass unit. Hence, they do 
not contribute much to an element’s overall atomic mass. Therefore, when 


considering atomic mass, it is customary to ignore the mass of any electrons 
and calculate the atom’s mass based on the number of protons and neutrons 
alone. Although not significant contributors to mass, electrons do contribute 
greatly to the atom’s charge, as each electron has a negative charge equal to 
the positive charge of a proton. In uncharged, neutral atoms, the number of 
electrons orbiting the nucleus is equal to the number of protons inside the 
nucleus. In these atoms, the positive and negative charges cancel each other 
out, leading to an atom with no net charge. 


Accounting for the sizes of protons, neutrons, and electrons, most of the 
volume of an atom—greater than 99 percent—is, in fact, empty space. With 
all this empty space, one might ask why so-called solid objects do not just 
pass through one another. The reason they do not is that the electrons that 
surround all atoms are negatively charged and negative charges repel each 
other. 


Protons, Neutrons, and Electrons 


Charge Mass (amu) Location 
Proton +] i. nucleus 
Neutron 0 1 nucleus 
Electron —1 0 orbitals 


Atomic Number and Mass 


Atoms of each element contain a characteristic number of protons and 
electrons. The number of protons determines an element’s atomic number 
and is used to distinguish one element from another. Thus, an atom with 
only one proton and one electron is always going to be an atom of 


hydrogen; an atom with two electrons and two protons is an atom of 
helium, etc. Unlike the fixed number of electrons and protons in atoms of 
any particular element, however, the number of neutrons is variable. An 
atom of hydrogen can have zero, one or two neutrons. Different numbers of 
neutrons will not change the charge, but will change the mass of an atom. 
These different forms, varying only in the number of neutrons, are called 
isotopes. Together, the number of protons and the number of neutrons 
determine an element’s mass number, as illustrated in [link]. Note that the 
small contribution of mass from electrons is disregarded in calculating the 
mass number. This approximation of mass can be used to easily calculate 
how many neutrons an element has by simply subtracting the number of 
protons from the mass number. Since an element’s isotopes will have 
different mass numbers, scientists also determine the relative atomic mass 
or standard atomic weight, which is the calculated mean of the mass 
numbers for its naturally occurring isotopes. Often, the resulting number 
contains a fraction. For example, the relative atomic mass of chlorine (Cl) is 
35.45 because chlorine is composed of several isotopes, some (the majority) 
with an atomic mass of 35 (17 protons and 18 neutrons) and some with an 
atomic mass of 37 (17 protons and 20 neutrons). 


Atomic number 


Mass number 


Carbon has an atomic number 
of six, and two stable isotopes 
with mass numbers of twelve 
and thirteen, respectively. Its 
relative atomic mass is 12.011. 


Isotopes 


Isotopes are different forms of an element that have the same number of 
protons but a different number of neutrons. Some elements—such as 
carbon, potassium, and uranium—have naturally occurring isotopes. 
Carbon-12 contains six protons, six neutrons, and six electrons; therefore, it 
has a mass number of 12 (six protons and six neutrons). Carbon-14 contains 
six protons, eight neutrons, and six electrons; its atomic mass is 14 (six 
protons and eight neutrons). These two alternate forms of carbon are 
isotopes. Many isotopes are stable, but others are unstable, and can lose 
neutrons, protons, and electrons, in order to attain a more stable atomic 
configuration (lower level of potential energy). These unstable isotopes are 
the radioactive isotopes, or radioisotopes. Radioactive decay (carbon-14 
losing neutrons to eventually become carbon-12) describes the energy loss 
that occurs when an unstable atom’s nucleus releases particles and 
radiation. 


Note: 

Evolution Connection 

Carbon Dating 

Carbon is normally present in the atmosphere in the form of gaseous 
compounds like carbon dioxide and methane. Carbon-14 ('4C) is a 
naturally occurring radioisotope that is created in the atmosphere from 
atmospheric !4N (nitrogen) by the addition of a neutron and the loss of a 
proton because of cosmic rays. This is a continuous process, so more !4C is 
always being created. As a living organism incorporates !4C initially as 
carbon dioxide fixed in the process of photosynthesis, the relative amount 
of /4C in its body is equal to the concentration of !4C in the atmosphere. 
When an organism dies, it is no longer ingesting '4C, so the ratio between 
'4C and !*C will decline as 4C decays gradually to '4N by a process called 
beta decay—the emission of electrons or positrons. This decay gives off 
energy in a slow process. 

After approximately 5,730 years, half of the starting concentration of 4C 
will have been converted back to ‘“N. The time it takes for half of the 
original concentration of an isotope to decay back to its more stable form is 


called its half-life. Because the half-life of !4C is long, it is used to date 
formerly living objects such as old bones or wood. Comparing the ratio of 
the '4C concentration found in an object to the amount of '4C detected in 
the atmosphere, the amount of the isotope that has not yet decayed can be 
determined. On the basis of this amount, the age of the material, such as 
the pygmy mammoth shown in [link], can be calculated with accuracy if it 
is not much older than about 50,000 years. Other elements have isotopes 
with different half lives. For example, *°K (potassium-40) has a half-life of 
1.25 billion years, and *?°U (Uranium 235) has a half-life of about 700 
million years. Through the use of radiometric dating, scientists can study 
the age of fossils or other remains of extinct organisms to understand how 
organisms have evolved from earlier species. 


The age of carbon-containing 
remains less than about 50,000 
years old, such as this pygmy 
mammoth, can be determined 
using carbon dating. (credit: Bill 
Faulkner, NPS) 


The Periodic Table 


The different elements are organized and displayed in the periodic table. 
Devised by Russian chemist Dmitri Mendeleev (1834—1907) in 1869, the 
table groups elements that, although unique, share certain chemical 
properties with other elements. The properties of elements are responsible 
for their physical state at room temperature: they may be gases, solids, or 
liquids. Elements also have specific chemical reactivity, the ability to 
combine and to chemically bond with each other. 


In the periodic table, shown in [link], the elements are organized and 
displayed according to their atomic number and are arranged in a series of 
rows and columns based on shared chemical and physical properties. In 
addition to providing the atomic number for each element, the periodic 
table also displays the element’s atomic mass. Looking at carbon, for 
example, its symbol (C) and name appear, as well as its atomic number of 
six (in the upper left-hand corner) and its relative atomic mass of 12.011. 


Periodic Table of the Elements 


[ 


fiona [_ ] Other non-metals |_| Noble gases 
Number ; j 
Symbol [_] Alkali metals {)] Lanthanides 
1.01 Relative {| Transition metals [D) Actinides 
Name Hydrogen Atomic Mass [_] Other metals [_] Unknown 


chemical 
properties 


[[] Alkaline earth metals 
|__| Halogens 


The periodic table shows the atomic mass and atomic number of 
each element. The atomic number appears above the symbol for 
the element and the approximate atomic mass appears below it. 


The periodic table groups elements according to chemical properties. The 
differences in chemical reactivity between the elements are based on the 
number and spatial distribution of an atom’s electrons. Atoms that 
chemically react and bond to each other form molecules. Molecules are 
simply two or more atoms chemically bonded together. Logically, when two 
atoms chemically bond to form a molecule, their electrons, which form the 
outermost region of each atom, come together first as the atoms form a 
chemical bond. 


Electron Shells and the Bohr Model 


It should be stressed that there is a connection between the number of 
protons in an element, the atomic number that distinguishes one element 
from another, and the number of electrons it has. In all electrically neutral 
atoms, the number of electrons is the same as the number of protons. Thus, 
each element, at least when electrically neutral, has a characteristic number 
of electrons equal to its atomic number. 


An early model of the atom was developed in 1913 by Danish scientist 
Niels Bohr (1885-1962). The Bohr model shows the atom as a central 
nucleus containing protons and neutrons, with the electrons in circular 
orbitals at specific distances from the nucleus, as illustrated in [link]. These 
orbits form electron shells or energy levels, which are a way of visualizing 
the number of electrons in the outermost shells. These energy levels are 
designated by a number and the symbol “n.” For example, 1n represents the 
first energy level located closest to the nucleus. 


The Bohr model was 
developed by Niels Bohrs in 
1913. In this model, electrons 
exist within principal shells. 

An electron normally exists 


in the lowest energy shell 
available, which is the one 
closest to the nucleus. Energy 
from a photon of light can 
bump it up to a higher energy 
Shell, but this situation is 
unstable, and the electron 
quickly decays back to the 
ground state. In the process, a 
photon of light is released. 


Electrons fill orbitals in a consistent order: they first fill the orbitals closest 
to the nucleus, then they continue to fill orbitals of increasing energy further 
from the nucleus. If there are multiple orbitals of equal energy, they will be 
filled with one electron in each energy level before a second electron is 
added. The electrons of the outermost energy level determine the energetic 
stability of the atom and its tendency to form chemical bonds with other 
atoms to form molecules. 


Under standard conditions, atoms fill the inner shells first, often resulting in 
a variable number of electrons in the outermost shell. The innermost shell 
has a maximum of two electrons but the next two electron shells can each 
have a maximum of eight electrons. This is known as the octet rule, which 
States, with the exception of the innermost shell, that atoms are more stable 
energetically when they have eight electrons in their valence shell, the 
outermost electron shell. Examples of some neutral atoms and their electron 
configurations are shown in [link]. Notice that in this [link], helium has a 
complete outer electron shell, with two electrons filling its first and only 
shell. Similarly, neon has a complete outer 2n shell containing eight 
electrons. In contrast, chlorine and sodium have seven and one in their outer 
shells, respectively, but theoretically they would be more energetically 
stable if they followed the octet rule and had eight. 


Bohr diagrams indicate how many electrons fill each 
principal shell. Group 18 elements (helium, neon, and 
argon are shown) have a full outer, or valence, shell. A 

full valence shell is the most stable electron 
configuration. Elements in other groups have partially 
filled valence shells and gain or lose electrons to 
achieve a stable electron configuration. 


Understanding that the organization of the periodic table is based on the 
total number of protons (and electrons) helps us know how electrons are 
distributed among the outer shell. The periodic table is arranged in columns 
and rows based on the number of electrons and where these electrons are 
located. Take a closer look at the some of the elements in the table’s far 
right column in [link]. The group 18 atoms helium (He), neon (Ne), and 
argon (Ar) all have filled outer electron shells, making it unnecessary for 
them to share electrons with other atoms to attain stability; they are highly 
stable as single atoms. Their non-reactivity has resulted in their being 
named the inert gases (or noble gases). Compare this to the group 1 
elements in the left-hand column. These elements, including hydrogen (H), 
lithium (Li), and sodium (Na), all have one electron in their outermost 


shells. That means that they can achieve a stable configuration and a filled 
outer shell by donating or sharing one electron with another atom or a 
molecule such as water. Hydrogen will donate or share its electron to 
achieve this configuration, while lithium and sodium will donate their 
electron to become stable. As a result of losing a negatively charged 
electron, they become positively charged ions. Group 17 elements, 
including fluorine and chlorine, have seven electrons in their outmost 
shells, so they tend to fill this shell with an electron from other atoms or 
molecules, making them negatively charged ions. Group 14 elements, of 
which carbon is the most important to living systems, have four electrons in 
their outer shell allowing them to make several covalent bonds (discussed 
below) with other atoms. Thus, the columns of the periodic table represent 
the potential shared state of these elements’ outer electron shells that is 
responsible for their similar chemical characteristics. 


Chemical Reactions and Molecules 


All elements are most stable when their outermost shell is filled with 
electrons according to the octet rule. This is because it is energetically 
favorable for atoms to be in that configuration and it makes them stable. 
However, since not all elements have enough electrons to fill their 
outermost shells, atoms form chemical bonds with other atoms thereby 
obtaining the electrons they need to attain a stable electron configuration. 
When two or more atoms chemically bond with each other, the resultant 
chemical structure is a molecule. The familiar water molecule, H>O, 
consists of two hydrogen atoms and one oxygen atom; these bond together 
to form water, as illustrated in [link]. Atoms can form molecules by 
donating, accepting, or sharing electrons to fill their outer shells. 


Two or more atoms may bond with each other to form 
a molecule. When two hydrogens and an oxygen share 
electrons via covalent bonds, a water molecule is 
formed. 


Chemical reactions occur when two or more atoms bond together to form 
molecules or when bonded atoms are broken apart. The substances used in 
the beginning of a chemical reaction are called the reactants (usually found 
on the left side of a chemical equation), and the substances found at the end 
of the reaction are known as the products (usually found on the right side 
of a chemical equation). An arrow is typically drawn between the reactants 
and products to indicate the direction of the chemical reaction; this direction 
is not always a “one-way street.” For the creation of the water molecule 
shown above, the chemical equation would be: 

Equation: 


An example of a simple chemical reaction is the breaking down of 
hydrogen peroxide molecules, each of which consists of two hydrogen 
atoms bonded to two oxygen atoms (H 70>). The reactant hydrogen 
peroxide is broken down into water, containing one oxygen atom bound to 
two hydrogen atoms (HO), and oxygen, which consists of two bonded 
oxygen atoms (O>). In the equation below, the reaction includes two 


hydrogen peroxide molecules and two water molecules. This is an example 
of a balanced chemical equation, wherein the number of atoms of each 
element is the same on each side of the equation. According to the law of 
conservation of matter, the number of atoms before and after a chemical 
reaction should be equal, such that no atoms are, under normal 
circumstances, created or destroyed. 

Equation: 


2H2O2 (hydrogen peroxide) —> 2H2O (water) + O, (oxygen) 


Even though all of the reactants and products of this reaction are molecules 
(each atom remains bonded to at least one other atom), in this reaction only 
hydrogen peroxide and water are representative of a subclass of molecules 
known as compounds: they contain atoms of more than one type of 
element. Molecular oxygen, on the other hand, as shown in [link], consists 
of two doubly bonded oxygen atoms and is not classified as a compound 
but as an element. 


The oxygen atoms in an O>) molecule are 
joined by a double bond. 


Some chemical reactions, such as the one shown above, can proceed in one 
direction until the reactants are all used up. The equations that describe 
these reactions contain a unidirectional arrow and are irreversible. 
Reversible reactions are those that can go in either direction. In reversible 
reactions, reactants are turned into products, but when the concentration of 
product goes beyond a certain threshold (characteristic of the particular 
reaction), some of these products will be converted back into reactants; at 


this point, the designations of products and reactants are reversed. This back 
and forth continues until a certain relative balance between reactants and 
products occurs—a state called equilibrium. These situations of reversible 
reactions are often denoted by a chemical equation with a double headed 
arrow pointing towards both the reactants and products. 


For example, in human blood, excess hydrogen ions (H") bind to 
bicarbonate ions (HCO3°) forming an equilibrium state with carbonic acid 
(H»CO3). If carbonic acid were added to this system, some of it would be 
converted to bicarbonate and hydrogen ions. 

Equation: 


HCO; + Ht © HCO; 


In biological reactions, however, equilibrium is rarely obtained because the 
concentrations of the reactants or products or both are constantly changing, 
often with a product of one reaction being a reactant for another. To return 
to the example of excess hydrogen ions in the blood, the formation of 
carbonic acid will be the major direction of the reaction. However, the 
carbonic acid can also leave the body as carbon dioxide gas (via exhalation) 
instead of being converted back to bicarbonate ion, thus driving the reaction 
to the right by the chemical law known as law of mass action. These 
reactions are important for maintaining the homeostasis of our blood. 
Equation: 


HCO; + Ht © H»CO3 © CQO, + H2O 


Ions and Ionic Bonds 


Some atoms are more stable when they gain or lose an electron (or possibly 
two) and form ions. This fills their outermost electron shell and makes them 
energetically more stable. Because the number of electrons does not equal 
the number of protons, each ion has a net charge. Cations are positive ions 
that are formed by losing electrons. Negative ions are formed by gaining 
electrons and are called anions. Anions are designated by their elemental 


name being altered to end in “-ide”: the anion of chlorine is called chloride, 
and the anion of sulfur is called sulfide, for example. 


This movement of electrons from one element to another is referred to as 
electron transfer. As [link] illustrates, sodium (Na) only has one electron in 
its outer electron shell. It takes less energy for sodium to donate that one 
electron than it does to accept seven more electrons to fill the outer shell. If 
sodium loses an electron, it now has 11 protons, 11 neutrons, and only 10 
electrons, leaving it with an overall charge of +1. It is now referred to as a 
sodium ion. Chlorine (Cl) in its lowest energy state (called the ground state) 
has seven electrons in its outer shell. Again, it is more energy-efficient for 
chlorine to gain one electron than to lose seven. Therefore, it tends to gain 
an electron to create an ion with 17 protons, 17 neutrons, and 18 electrons, 
giving it a net negative (—1) charge. It is now referred to as a chloride ion. 
In this example, sodium will donate its one electron to empty its shell, and 
chlorine will accept that electron to fill its shell. Both ions now satisfy the 
octet rule and have complete outermost shells. Because the number of 
electrons is no longer equal to the number of protons, each is now an ion 
and has a +1 (sodium cation) or —1 (chloride anion) charge. Note that these 
transactions can normally only take place simultaneously: in order for a 
sodium atom to lose an electron, it must be in the presence of a suitable 
recipient like a chlorine atom. 


In the formation of an ionic compound, 
metals lose electrons and nonmetals gain 
electrons to achieve an octet. 


Ionic bonds are formed between ions with opposite charges. For instance, 
positively charged sodium ions and negatively charged chloride ions bond 


together to make crystals of sodium chloride, or table salt, creating a 
crystalline molecule with zero net charge. 


Certain salts are referred to in physiology as electrolytes (including sodium, 
potassium, and calcium), ions necessary for nerve impulse conduction, 
muscle contractions and water balance. Many sports drinks and dietary 
supplements provide these ions to replace those lost from the body via 
sweating during exercise. 


Covalent Bonds and Other Bonds and Interactions 


Another way the octet rule can be satisfied is by the sharing of electrons 
between atoms to form covalent bonds. Covalent bonds are much more 
common than ionic bonds in the molecules of living organisms, and often 
the covalent bonds discussed in these systems are stronger than the ionic 
bonds. So, Biologists often think of covalent bonds as being stronger than 
ionic bonds, in fact, ionic bonds can produce some of the strongest bonds 
on the planet i.e. steel. Since covalent bonds are commonly found in 
carbon-based organic molecules, such as carbohydrates, our DNA and 
proteins are the bonds we discuss most, and covalent bonds are also found 
in inorganic molecules like H»O, CO», and Op», Biologists often think of 
covalent bonds begin the strongest. In addition, One, two, or three pairs of 
electrons may be shared, making single, double, and triple bonds, 
respectively. The more covalent bonds between two atoms, the stronger 
their connection. Thus, triple bonds are the strongest in biologic systems. 


The strength of different levels of covalent bonding is one of the main 
reasons living organisms have a difficult time in acquiring nitrogen for use 
in constructing their molecules, even though molecular nitrogen, No, is the 
most abundant gas in the atmosphere. Molecular nitrogen consists of two 
nitrogen atoms triple bonded to each other and, as with all molecules, the 
sharing of these three pairs of electrons between the two nitrogen atoms 
allows for the filling of their outer electron shells, making the molecule 
more stable than the individual nitrogen atoms. This strong triple bond 
makes it difficult for living systems to break apart this nitrogen in order to 
use it as constituents of proteins and DNA. 


The formation of water molecules provides an example of covalent 
bonding. The hydrogen and oxygen atoms that combine to form water 
molecules are bound together by covalent bonds, as shown in [link]. The 
electron from the hydrogen splits its time between the incomplete outer 
shell of the hydrogen atoms and the incomplete outer shell of the oxygen 
atoms. To completely fill the outer shell of oxygen, which has six electrons 
in its outer shell but which would be more stable with eight, two electrons 
(one from each hydrogen atom) are needed: hence the well-known formula 
H,O. The electrons are shared between the two elements to fill the outer 
shell of each, making both elements more stable. 


Polar Covalent Bonds 


There are two types of covalent bonds: polar and nonpolar. In a polar 
covalent bond, shown in [link], the electrons are unequally shared by the 
atoms and are attracted more to one nucleus than the other. Because of the 
unequal distribution of electrons between the atoms of different elements, a 
slightly positive (6+) or slightly negative (6—) charge develops. This partial 
charge is an important property of water and accounts for many of its 
characteristics. 


Water is a polar molecule, with the hydrogen atoms acquiring a partial 
positive charge and the oxygen a partial negative charge. This occurs 
because the nucleus of the oxygen atom is more attractive to the electrons 
of the hydrogen atoms than the hydrogen nucleus is to the oxygen’s 
electrons. Thus oxygen has a higher electronegativity than hydrogen and 
the shared electrons spend more time in the vicinity of the oxygen nucleus 
than they do near the nucleus of the hydrogen atoms, giving the atoms of 
oxygen and hydrogen slightly negative and positive charges, respectively. 
Another way of stating this is that the probability of finding a shared 
electron near an oxygen nucleus is more likely than finding it near a 
hydrogen nucleus. Either way, the atom’s relative electronegativity 
contributes to the development of partial charges whenever one element is 
significantly more electronegative than the other, and the charges generated 
by these polar bonds may then be used for the formation of hydrogen bonds 
based on the attraction of opposite partial charges. (Hydrogen bonds, which 


are discussed in detail below, are weak bonds between slightly positively 
charged hydrogen atoms to slightly negatively charged atoms in other 
molecules.) Since macromolecules often have atoms within them that differ 
in electronegativity, polar bonds are often present in organic molecules. 


Nonpolar Covalent Bonds 


Nonpolar covalent bonds form between two atoms of the same element or 
between different elements that share electrons equally. For example, 
molecular oxygen (O2) is nonpolar because the electrons will be equally 
distributed between the two oxygen atoms. 


Another example of a nonpolar covalent bond is methane (CH,), also 
shown in [link]. Carbon has four electrons in its outermost shell and needs 
four more to fill it. It gets these four from four hydrogen atoms, each atom 
providing one, making a stable outer shell of eight electrons. Carbon and 
hydrogen do not have the same electronegativity but are similar; thus, 
nonpolar bonds form. The hydrogen atoms each need one electron for their 
outermost shell, which is filled when it contains two electrons. These 
elements share the electrons equally among the carbons and the hydrogen 
atoms, creating a nonpolar covalent molecule. 


Bond type Molecular shape Molecular type 


+ 3+ 


Polar covalent 


Carbon 
dioxide 
Polar covalent Linear 


Whether a molecule is polar or nonpolar 
depends both on bond type and molecular 
shape. Both water and carbon dioxide have 
polar covalent bonds, but carbon dioxide is 
linear, so the partial charges on the molecule 
cancel each other out. 


Hydrogen Bonds and Van Der Waals Interactions 


Ionic and covalent bonds between elements require energy to break. Ionic 
bonds are not as strong as covalent, which determines their behavior in 
biological systems. However, not all bonds are ionic or covalent bonds. 
Weaker bonds can also form between molecules. Two weak bonds that 
occur frequently are hydrogen bonds and van der Waals interactions. 
Without these two types of bonds, life as we know it would not exist. 
Hydrogen bonds provide many of the critical, life-sustaining properties of 


water and also stabilize the structures of proteins and DNA, the building 
block of cells. 


When polar covalent bonds containing hydrogen form, the hydrogen in that 
bond has a slightly positive charge because hydrogen’s electron is pulled 
more strongly toward the other element and away from the hydrogen. 
Because the hydrogen is slightly positive, it will be attracted to neighboring 
negative charges. When this happens, a weak interaction occurs between the 
6‘ of the hydrogen from one molecule and the é— charge on the more 
electronegative atoms of another molecule, usually oxygen or nitrogen, or 
within the same molecule. This interaction is called a hydrogen bond. This 
type of bond is common and occurs regularly between water molecules. 
Individual hydrogen bonds are weak and easily broken; however, they occur 
in very large numbers in water and in organic polymers, creating a major 
force in combination. Hydrogen bonds are also responsible for zipping 
together the DNA double helix. 


Like hydrogen bonds, van der Waals interactions are weak attractions or 
interactions between molecules. Van der Waals attractions can occur 
between any two or more molecules and are dependent on slight 
fluctuations of the electron densities, which are not always symmetrical 
around an atom. For these attractions to happen, the molecules need to be 
very close to one another. These bonds, along with hydrogen bonds, help 
form the three-dimensional structure of the proteins in our cells that is 
necessary for their proper function. 


Water: the Molecule of Life 


Introduction 

"Life can be thought of as water kept in the right temperature in the right 
atmosphere in the right light for a long enough period of time." Norman J. 
Berrill, You and the Universe, pg. 45, 1958 


Why do scientists spend time looking for water on other planets? Why is 
water so important? It is because water is essential to life as we know it. 
Water is one of the more abundant molecules and the one most critical to 
life on Earth. Approximately 70 percent of the human body is made up of 
water. Without it, life as we know it simply would not exist. 


The polarity of the water molecule and its resulting hydrogen bonding 
make water a unique substance with special properties that are intimately 
tied to the processes of life. Life originally evolved in a watery 
environment, and most of an organism’s cellular chemistry and metabolism 
occur inside the watery contents of the cell’s cytoplasm. Special properties 
of water are its high heat capacity and heat of vaporization, its ability to 
dissolve polar molecules, its cohesive and adhesive properties, and its 
dissociation into ions that leads to the generation of pH. Understanding 
these characteristics of water helps to elucidate its importance in 
maintaining life. 


Water’s Polarity 


One of water’s important properties is that it is composed of polar 
molecules: the hydrogen and oxygen within water molecules (H.O) form 
polar covalent bonds. While there is no net charge to a water molecule, the 
polarity of water creates a slightly positive charge on hydrogen and a 
slightly negative charge on oxygen, contributing to water’s properties of 
attraction. Water’s charges are generated because oxygen is more 
electronegative than hydrogen, making it more likely that a shared electron 
would be found near the oxygen nucleus than the hydrogen nucleus, thus 
generating the partial negative charge near the oxygen. 


As a result of water’s polarity, each water molecule attracts other water 
molecules because of the opposite charges between water molecules, 
forming hydrogen bonds. Water also attracts or is attracted to other polar 
molecules and ions. A polar substance that interacts readily with or 
dissolves in water is referred to as hydrophilic (hydro- = “water”; -philic = 
“loving”). In contrast, non-polar molecules such as oils and fats do not 
interact well with water, as shown in [link] and separate from it rather than 
dissolve in it, as we see in salad dressings containing oil and vinegar (an 
acidic water solution). These nonpolar compounds are called hydrophobic 
(hydro- = “water”; -phobic = “fearing”). 


Oil and water do not mix. As this 
macro image of oil and water 
shows, oil does not dissolve in 
water but forms droplets instead. 
This is due to it being a nonpolar 
compound. (credit: Gautam 
Dogra). 


Water’s States: Gas, Liquid, and Solid 


The formation of hydrogen bonds is an important quality of the liquid water 
that is crucial to life as we know it. As water molecules make hydrogen 
bonds with each other, water takes on some unique chemical characteristics 
compared to other liquids and, since living things have a high water 
content, understanding these chemical features is key to understanding life. 
In liquid water, hydrogen bonds are constantly formed and broken as the 
water molecules slide past each other. The breaking of these bonds is 
caused by the motion (kinetic energy) of the water molecules due to the 
heat contained in the system. When the heat is raised as water is boiled, the 
higher kinetic energy of the water molecules causes the hydrogen bonds to 
break completely and allows water molecules to escape into the air as gas 
(steam or water vapor). On the other hand, when the temperature of water is 
reduced and water freezes, the water molecules form a crystalline structure 
maintained by hydrogen bonding (there is not enough energy to break the 
hydrogen bonds) that makes ice less dense than liquid water, a phenomenon 
not seen in the solidification of other liquids. 


Water’s lower density in its solid form is due to the way hydrogen bonds are 
oriented as it freezes: the water molecules are pushed farther apart 
compared to liquid water. With most other liquids, solidification when the 
temperature drops includes the lowering of kinetic energy between 
molecules, allowing them to pack even more tightly than in liquid form and 
giving the solid a greater density than the liquid. 


The lower density of ice, illustrated and pictured in [link], an anomaly, 
causes it to float at the surface of liquid water, such as in an iceberg or in 
the ice cubes in a glass of ice water. In lakes and ponds, ice will form on the 
surface of the water creating an insulating barrier that protects the animals 
and plant life in the pond from freezing. Without this layer of insulating ice, 
plants and animals living in the pond would freeze in the solid block of ice 
and could not survive. The detrimental effect of freezing on living 
organisms is caused by the expansion of ice relative to liquid water. The ice 
crystals that form upon freezing rupture the delicate membranes essential 
for the function of living cells, irreversibly damaging them. Cells can only 
survive freezing if the water in them is temporarily replaced by another 
liquid like glycerol. 


Hydrogen bonding makes ice less dense than liquid 
water. The (a) lattice structure of ice makes it less 
dense than the freely flowing molecules of liquid 

water, enabling it to (b) float on water. (credit a: 
modification of work by Jane Whitney, image created 
using Visual Molecular Dynamics (VMD) 


software! !otmote!. credit b: courtesy David A. Rintoul) 

W. Humphrey W., A. Dalke, and K. Schulten, “VMD 

—Visual Molecular Dynamics,” Journal of Molecular 
Graphics 14 (1996): 33-38. 


Water’s High Heat Capacity 


Water’s high heat capacity is a property caused by hydrogen bonding 
among water molecules. Water has the highest specific heat capacity of any 
liquids. Specific heat is defined as the amount of heat one gram of a 
substance must absorb or lose to change its temperature by one degree 
Celsius. For water, this amount is one calorie. It therefore takes water a long 
time to heat and long time to cool. In fact, the specific heat capacity of 
water is about five times more than that of sand. This explains why the land 
cools faster than the sea. Due to its high heat capacity, water is used by 
warm blooded animals to more evenly disperse heat in their bodies: it acts 
in a similar manner to a car’s cooling system, transporting heat from warm 
places to cool places, causing the body to maintain a more even 
temperature. 


Water’s Heat of Vaporization 


Water also has a high heat of vaporization, the amount of energy required 
to change one gram of a liquid substance to a gas. A considerable amount of 
heat energy (586 cal) is required to accomplish this change in water. This 
process occurs on the surface of water. As liquid water heats up, hydrogen 
bonding makes it difficult to separate the liquid water molecules from each 
other, which is required for it to enter its gaseous phase (steam). As a result, 
water acts as a heat sink or heat reservoir and requires much more heat to 
boil than does a liquid such as ethanol (grain alcohol), whose hydrogen 
bonding with other ethanol molecules is weaker than water’s hydrogen 
bonding. Eventually, as water reaches its boiling point of 100° Celsius 
(212° Fahrenheit), the heat is able to break the hydrogen bonds between the 
water molecules, and the kinetic energy (motion) between the water 
molecules allows them to escape from the liquid as a gas. Even when below 
its boiling point, water’s individual molecules acquire enough energy from 
other water molecules such that some surface water molecules can escape 
and vaporize: this process is known as evaporation. 


The fact that hydrogen bonds need to be broken for water to evaporate 
means that a substantial amount of energy is used in the process. As the 
water evaporates, energy is taken up by the process, cooling the 
environment where the evaporation is taking place. In many living 
organisms, including in humans, the evaporation of sweat, which is 90 
percent water, allows the organism to cool so that homeostasis of body 
temperature can be maintained. 


Water’s Solvent Properties 


Since water is a polar molecule with slightly positive and slightly negative 
charges, ions and polar molecules can readily dissolve in it. Therefore, 
water is referred to as a solvent, a substance capable of dissolving other 
polar molecules and ionic compounds. The charges associated with these 
molecules will form hydrogen bonds with water, surrounding the particle 
with water molecules. This is referred to as a sphere of hydration, or a 
hydration shell, as illustrated in [link] and serves to keep the particles 
separated or dispersed in the water. 


When ionic compounds are added to water, the individual ions react with 
the polar regions of the water molecules and their ionic bonds are disrupted 
in the process of dissociation. Dissociation occurs when atoms or groups of 
atoms break off from molecules and form ions. Consider table salt (NaCl, or 
sodium chloride): when NaCl crystals are added to water, the molecules of 
NaCl] dissociate into Na* and Cl ions, and spheres of hydration form 
around the ions, illustrated in [link]. The positively charged sodium ion is 
surrounded by the partially negative charge of the water molecule’s oxygen. 
The negatively charged chloride ion is surrounded by the partially positive 
charge of the hydrogen on the water molecule. 


When table salt (NaCl) is 
mixed in water, spheres of 
hydration are formed around 
the ions. 


Water’s Cohesive and Adhesive Properties 


Have you ever filled a glass of water to the very top and then slowly added 
a few more drops? Before it overflows, the water forms a dome-like shape 
above the rim of the glass. This water can stay above the glass because of 
the property of cohesion. In cohesion, water molecules are attracted to each 
other (because of hydrogen bonding), keeping the molecules together at the 
liquid-gas (water-air) interface, although there is no more room in the glass. 


Cohesion allows for the development of surface tension, the capacity of a 
substance to withstand being ruptured when placed under tension or stress. 


This is also why water forms droplets when placed on a dry surface rather 
than being flattened out by gravity. When a small scrap of paper is placed 
onto the droplet of water, the paper floats on top of the water droplet even 
though paper is denser (heavier) than the water. Cohesion and surface 
tension keep the hydrogen bonds of water molecules intact and support the 
item floating on the top. It’s even possible to “float” a needle on top of a 
glass of water if it is placed gently without breaking the surface tension, as 
shown in [link]. 


The weight of the needle is pulling 
the surface downward; at the same 
time, the surface tension is pulling 
it up, suspending it on the surface 
of the water and keeping it from 
sinking. Notice the indentation in 
the water around the needle. 
(credit: Cory Zanker) 


These cohesive forces are related to water’s property of adhesion, or the 
attraction between water molecules and other molecules. This attraction is 
sometimes stronger than water’s cohesive forces, especially when the water 
is exposed to charged surfaces such as those found on the inside of thin 
glass tubes known as capillary tubes. Adhesion is observed when water 


“climbs” up the tube placed in a glass of water: notice that the water 
appears to be higher on the sides of the tube than in the middle. This is 
because the water molecules are attracted to the charged glass walls of the 
capillary more than they are to each other and therefore adhere to it. This 
type of adhesion is called capillary action, and is illustrated in [link]. 


Capillary tube 


_ 


Capillary 
attraction 


Capillary action in a glass tube is 
caused by the adhesive forces 
exerted by the internal surface of 
the glass exceeding the cohesive 
forces between the water 
molecules themselves. (credit: 
modification of work by Pearson- 
Scott Foresman, donated to the 
Wikimedia Foundation) 


Why are cohesive and adhesive forces important for life? Cohesive and 
adhesive forces are important for the transport of water from the roots to the 


leaves in plants. These forces create a “pull” on the water column. This pull 
results from the tendency of water molecules being evaporated on the 
surface of the plant to stay connected to water molecules below them, and 
so they are pulled along. Plants use this natural phenomenon to help 
transport water from their roots to their leaves. Without these properties of 
water, plants would be unable to receive the water and the dissolved 
minerals they require. In another example, insects such as the water strider, 
shown in [link], use the surface tension of water to stay afloat on the surface 
layer of water and even mate there. 


Water’s cohesive and adhesive 
properties allow this water strider 
(Gerris sp.) to stay afloat. (credit: 

Tim Vickers) 


pH, Acids, and Bases 


The pH of a solution indicates its acidity or alkalinity. 
Equation: 


H,O(I) «+ Ht (aq) + OH (aq) 


Litmus or pH paper, filter paper that has been treated with a natural water- 
soluble dye so it can be used as a pH indicator, to test how much acid 
(acidity) or base (alkalinity) exists in a solution. You might have even used 
some to test whether the water in a swimming pool is properly treated. In 
both cases, the pH test measures the concentration of hydrogen ions in a 
given solution. 


Hydrogen ions are spontaneously generated in pure water by the 
dissociation (ionization) of a small percentage of water molecules into 
equal numbers of hydrogen (H") ions and hydroxide (OH’) ions. While the 
hydroxide ions are kept in solution by their hydrogen bonding with other 
water molecules, the hydrogen ions, consisting of naked protons, are 
immediately attracted to un-ionized water molecules, forming hydronium 
ions (H30°). Still, by convention, scientists refer to hydrogen ions and their 
concentration as if they were free in this state in liquid water. 


The concentration of hydrogen ions dissociating from pure water is 1 x 1077 
moles H* ions per liter of water. Moles (mol) are a way to express the 
amount of a substance (which can be atoms, molecules, ions, etc), with one 
mole being equal to 6.02 x 10*° particles of the substance. Therefore, 1 
mole of water is equal to 6.02 x 107? water molecules. The pH is calculated 
as the negative of the base 10 logarithm of this concentration (see below). 
The logi9 of 1 x 10°” is -7.0, and the negative of this number (indicated by 
the “p” of “pH”) yields a pH of 7.0, which is also known as neutral pH. The 
pH inside of human cells and blood are examples of two areas of the body 
where near-neutral pH is maintained. 


pH = -log;)[Hydrogen Ion] 


Non-neutral pH readings result from dissolving acids or bases in water. 
Using the negative logarithm to generate positive integers, high 
concentrations of hydrogen ions yield a low pH number, whereas low levels 
of hydrogen ions result in a high pH. An acid is a substance that increases 
the concentration of hydrogen ions (H‘) in a solution, usually by having one 
of its hydrogen atoms dissociate. A base provides either hydroxide ions 
(OH_) or other negatively charged ions that combine with hydrogen ions, 
reducing their concentration in the solution and thereby raising the pH. In 


cases where the base releases hydroxide ions, these ions bind to free 
hydrogen ions, generating new water molecules. 


The stronger the acid, the more readily it donates H*. For example, 
hydrochloric acid (HCl) completely dissociates into hydrogen and chloride 
ions and is highly acidic, whereas the acids in tomato juice or vinegar do 
not completely dissociate and are considered weak acids. Conversely, 
strong bases are those substances that readily donate OH or take up 
hydrogen ions. Sodium hydroxide (NaOH) and many household cleaners 
are highly alkaline and give up OH™ rapidly when placed in water, thereby 
raising the pH. An example of a weak basic solution is seawater, which has 
a pH near 8.0, close enough to neutral pH that marine organisms adapted to 
this saline environment are able to thrive in it. 


The pH scale is, as previously mentioned, an inverse logarithm and ranges 
from 0 to 14 ([link]). Anything below 7.0 (ranging from 0.0 to 6.9) is 
acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline. Extremes in 
PH in either direction from 7.0 are usually considered inhospitable to life. 
The pH inside cells (6.8) and the pH in the blood (7.4) are both very close 
to neutral. However, the environment in the stomach is highly acidic, with a 
PH of 1 to 2. So how do the cells of the stomach survive in such an acidic 
environment? How do they homeostatically maintain the near neutral pH 
inside them? The answer is that they cannot do it and are constantly dying. 
New stomach cells are constantly produced to replace dead ones, which are 
digested by the stomach acids. It is estimated that the lining of the human 
stomach is completely replaced every seven to ten days. 


13 Bleach 
12 Soapy water 
11 Ammonia solution 
10 Milk of magnesia 
9 Baking soda 
8 Sea water 
7 Distilled water 
6 Urine 
5 Black coffee 
4 Tomato juice 
3 Orange juice 
2 Lemon juice 
1 Gastric acid 
0 


The pH scale measures the 
concentration of hydrogen 
ions (H*) in a solution. 
(credit: modification of work 
by Edward Stevens) 


Introduction to Biological Molecules 


Introduction 

"The most fundamental difference between compounds of low molecular 
weight and macromolecular compounds resides in the fact that the latter 
may exhibit properties that cannot be deduced from a close examination of 
the low molecular weight materials. Not very different structures can be 
obtained from a few building blocks, but if 10,000 or 100,000 bloocks are 
at hand, the most varied structures become possible..." Hermann Staudinger, 
quoted in R. Oesper, The Human Side of Scientists, pg. 75, 1975 


Biological macromolecules are large molecules, necessary for life (Table 
1), and these large molecules are made from smaller organic molecules. As 
noted above, there is an almost infinite variety of possible structures for 
macromolecules, since both the composition and the bonds lining the 
components can vary tremendously. There are four major classes of 
biological macromolecules (carbohydrates, lipids, proteins, and nucleic 
acids). As we explore these molecules, think about how each class makes 
up important cell components and perform a wide array of functions. Since 
all these biological macromolecules contain carbon, we call them are 
organic molecules. In addition, the ratio of carbon, hydrogen, oxygen, 
nitrogen, and additional minor elements determines the class of biological 
molecules. 


Type of Function Location in Cell 
Molecule 

Carbohydrates 

Simple Sugars Provide Quick Energy Cytoplasm 
Complex Support Cells (cellulose, Cell Walls 


Carbohydrates chitin); Store energy (cellulose, 


(cellulose, 
chitin, starch, 


glycogen) 


Lipids 


Triglycerides 
(fats and oils) 


Phospholipids 


Sterols and 
Steroids 


Waxes 


Proteins 


Nucleic Acids 
(DNA and 
RNA) 


(starch, glycogen) 


Store Energy 


Major component of 
biological membranes 


Stabilize animal plasma 
membranes; sex 
hormones 


Waterproofing 


Movement, Immunity, 
Energy Source, 
Enzymes, Structural 
Support, 
Communication, 
Hormones, 


Store and use genetic 
information 


A summary of the Biological Molecules 


chitin); 
cytoplasm 
(starch, 
glycogen) 


Cytoplasm 


Plasma 
membranes 


animal plasma 
membranes 


Cell Walls 
(plants),Excreted 
(animals) 


In all parts of the 
cell 


DNA (Nucleus) 
RNA 
(Cytoplasm, and 
Rough 
Endoplasmic 
Reticulum 


Chemical Reactions of Biological Macromolecules 


Condensation Reaction 


Most macromolecules are made from single subunits, or building blocks, 
called monomers. The monomers combine with each other using covalent 
bonds to form larger molecules known as polymers. In doing so, monomers 
release water molecules as byproducts. This type of reaction is known as 
condensation reaction. 


CH20OH CH20H CH20H CH20H 


fe) fe) OH H Oo 
H - OH 
+ —> + H20 
HO OH HO OH HO O H 
OH OH OH OH 


In the condensation reaction depicted above, two molecules of 
glucose are linked together to form the dissacharide maltose. In the 
process, a water molecule is formed. 


In a condensation reaction ({link]), the hydrogen of one monomer combines 
with the hydroxyl group of another monomer, releasing a molecule of water. 
At the same time, the monomers share electrons and form covalent bonds. 
As additional monomers join, this chain of repeating monomers forms a 
polymer. Different types of monomers can combine in many configurations, 
giving rise to a diverse group of macromolecules. Even one kind of 
monomer can combine in a variety of ways to form several different 
polymers: for example, glucose monomers are the constituents of starch, 
glycogen, and cellulose. 


Hydrolysis 


Polymers are broken down into monomers in a process known as 
hydrolysis, which means “to split water,” a reaction in which a water 
molecule is used during the breakdown ([link]). During these reactions, the 
polymer is broken into two components: one part gains a hydrogen atom 
(H+) and the other gains a hydroxyl molecule (OH—) from a split water 
molecule. 


CH,OH CH,OH CH,OH CH,OH 


OH H O OH O 
OH H 
O 
H H 
HO O oy 1° OH 
OH OH OH OH 


In the hydrolysis reaction shown here, the disaccharide maltose is 
broken down to form two glucose monomers. Note that this reaction 
is the reverse of the condensation reaction shown in [link]. 


Condensation and hydrolysis reactions are catalyzed, or “sped up,” by 
specific enzymes; condensation reactions involve the formation of new 
bonds, requiring energy, while hydrolysis reactions break bonds and release 
energy. These reactions are similar for most macromolecules, but each 
monomer and polymer reaction is specific for its class. For example, in our 
bodies, food is hydrolyzed, or broken down, into smaller molecules by 
catalytic enzymes in the digestive system. This allows for easy absorption 
of nutrients by cells in the intestine. Each macromolecule is broken down 
by a specific enzyme. For instance, carbohydrates are broken down by 
amylase, sucrase, lactase, or maltase. Proteins are broken down by the 
enzymes pepsin and peptidase, and by hydrochloric acid. Lipids are broken 
down by lipases. Breakdown of these macromolecules provides energy for 
cellular activities. 


Carbohydrates 


Introduction 

"T called it ignose, not knowing which carbohydrate it was. This name was 
turned down by my editor. 'God-nose' was not more successful, so in the 
end 'hexuronic acid' was agreed upon. To-day the substance is called 
‘ascorbic acid' and I will use this name." Albert Szent-Gyorgyi, Studies on 
Biological Oxidation and Some of its Catalysts (C4 Dicarboxylic Acids, 
Vitamin C and P Etc.), pg. 73, 1937 


Most people(except perhaps Szent-Gyorgyi's editor) are familiar with 
carbohydrates, one type of macromolecule, especially when it comes to 
what we eat. To lose weight, some individuals adhere to “low-carb” diets. 
Athletes, in contrast, often “carb-load” before important competitions to 
ensure that they have enough energy to compete at a high level. 
Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and 
vegetables are all natural sources of carbohydrates. Carbohydrates provide 
energy to the body, particularly through glucose, a simple sugar that is a 
component of starch and an ingredient in many staple foods. Carbohydrates 
also have other important functions in humans, animals, and plants. And, as 
you can infer from the epigraph above, the suffix "-ose" is a good clue that 
a word describes a carboydrate of some sort. 


Molecular Structures 


Carbohydrates can be represented by the stoichiometric formula (CH)0),, 
where n is the number of carbons in the molecule. In other words, the ratio 
of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. This 
formula also explains the origin of the term “carbohydrate”: the 
components are carbon (“carbo”) and the components of water (hence, 
“hydrate’”). Carbohydrates are classified into three subtypes: 
monosaccharides, disaccharides, and polysaccharides. 


Monosaccharides 


Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, 
the most common of which is glucose. In monosaccharides, the number of 
carbons usually ranges from three to seven. Most monosaccharide names 
end with the suffix -ose. Depending on the number of carbons in the sugar, 
they also may be known as trioses (three carbons), pentoses (five carbons), 
and or hexoses (six carbons). See [link] for an illustration of the 
monosaccharides. 


MONOSACCHARIDES 


Glyceraldehyde Dihydroxyacetone 


Ribose 


Monosaccharides are classified based on the 
position of their carbonyl group and the 
number of carbons in the backbone. Aldoses 


have a carbonyl group (indicated in green) at 
the end of the carbon chain, and ketoses 
have a carbonyl group in the middle of the 
carbon chain. Trioses, pentoses, and hexoses 
have three, five, and six carbon backbones, 
respectively. 


The chemical formula for glucose is CgH; 0g. In humans, glucose is an 
important source of energy. During cellular respiration, energy is released 
from glucose, and that energy is used to help make adenosine triphosphate 
(ATP). Plants synthesize glucose using carbon dioxide and water, and 
glucose in turn is used for energy requirements for the plant. Excess glucose 
is often stored as starch that is catabolized (the breakdown of larger 
molecules by cells) by humans and other animals that feed on plants. 


Galactose (part of lactose, or milk sugar) and fructose (found in sucrose, in 
fruit) are other common monosaccharides. Although glucose, galactose, and 
fructose all have the same chemical formula (CgH, Og), they differ 
structurally and chemically (and are known as isomers) because of the 
different arrangement of functional groups around the asymmetric carbon; 
all of these monosaccharides have more than one asymmetric carbon 
(Llink]). 


Glucose Galactose Fructose 


Glucose, galactose, and fructose are all 
hexoses. They are structural isomers, 
meaning they have the same chemical 

formula (CgH; O¢) but a different 
arrangement of atoms. 


Monosaccharides can exist as a linear chain or as ring-shaped molecules; in 
aqueous solutions they are usually found in ring forms ({link]). Glucose in a 
ring form can have two different arrangements of the hydroxyl group (OH) 
around the anomeric carbon (carbon 1 that becomes asymmetric in the 
process of ring formation). If the hydroxyl group is below carbon number 1 
in the sugar, it is said to be in the alpha (a) position, and if it is above the 
plane, it is said to be in the beta () position. 


Conversion between Linear and Ring Forms of Glucose 


Glucose 


CH,OH 


a Glucose 


CH,OH 


Fructose 


Five and six carbon monosaccharides exist 
in equilibrium between linear and ring 
forms. When the ring forms, the side chain it 
closes on is locked into an a or f position. 
Fructose and ribose also form rings, 
although they form five-membered rings as 
opposed to the six-membered ring of 
glucose. 


Disaccharides 


Disaccharides (di- = “two”) form when two monosaccharides undergo a 
condensation reaction (also known as a dehydration synthesis). During this 
process, the hydroxyl group of one monosaccharide combines with the 
hydrogen of another monosaccharide, releasing a molecule of water and 
forming a covalent bond. A covalent bond formed between a carbohydrate 
molecule and another molecule (in this case, between two 
monosaccharides) is known as a glycosidic bond ([link]). Glycosidic bonds 
(also called glycosidic linkages) can be of the alpha or the beta type. 


H OH 
Glucose 


CH,OH 


H OH f 


Sucrose Glycosidic Bond 


Sucrose is formed when a monomer of 
glucose and a monomer of fructose are 
joined in a condensation reaction to form a 
glycosidic bond. In the process, a water 
molecule is lost. By convention, the carbon 
atoms in a monosaccharide are numbered 


from the terminal carbon closest to the 

carbonyl] group. In sucrose, a glycosidic 

linkage is formed between carbon 1 in 
glucose and carbon 2 in fructose. 


Common disaccharides include lactose, maltose, and sucrose ((link]). 
Lactose is a disaccharide consisting of the monomers glucose and galactose. 
It is found naturally in milk. Maltose, or malt sugar, is a disaccharide 
formed by a condensation reaction between two glucose molecules. The 
most common disaccharide is sucrose, or table sugar, which is composed of 
the monomers glucose and fructose. 


CH,OH CH,OH 


Maltose 


CH,OH 
1) 
OH 
CH,OH 
OH 
[@) 
OH Oo 
OH 
OH 
Lactose OH 
CH,OH 
CH,OH 
Oo OH 
H HO 
CH,OH 
H OH OH H 


Sucrose 


Common disaccharides include maltose 
(grain sugar), lactose (milk sugar), and 
sucrose (table sugar). 


Polysaccharides 


A long chain of monosaccharides linked by glycosidic bonds is known as a 
polysaccharide (poly- = “many”). The chain may be branched or 
unbranched, and it may contain different types of monosaccharides. The 
molecular weight may be 100,000 daltons or more depending on the 
number of monomers joined. Starch, glycogen, cellulose, and chitin are 
primary examples of polysaccharides. 


Starch is the stored form of sugars in plants and is made up of a mixture of 
amylose and amylopectin (both polymers of glucose). Plants are able to 
synthesize glucose, and the excess glucose, beyond the plant’s immediate 
energy needs, is stored as starch in different plant parts, including roots and 
seeds. The starch in the seeds provides food for the embryo as it germinates 
and can also act as a source of food for humans and animals. The starch that 
is consumed by humans is broken down by enzymes, such as salivary 
amylases, into smaller molecules, such as maltose and glucose. The cells 
can then absorb the glucose. 


Starch is made up of glucose monomers that are joined by a 1-4 or a 1-6 
glycosidic bonds. The numbers 1-4 and 1-6 refer to the carbon number of 
the two residues that have joined to form the bond. As illustrated in [link], 
amylose is starch formed by unbranched chains of glucose monomers (only 
a 1-4 linkages), whereas amylopectin is a branched polysaccharide (a 1-6 
linkages at the branch points). 


Amylopectin 


Amylose and amylopectin are two different 
forms of starch. Amylose is composed of 
unbranched chains of glucose monomers 

connected by a 1,4 glycosidic linkages. 
Amylopectin is composed of branched 

chains of glucose monomers connected by a 

1,4 and a 1,6 glycosidic linkages. Because 


of the way the subunits are joined, the 
glucose chains have a helical structure. 
Glycogen (not shown) is similar in structure 
to amylopectin but more highly branched. 


Glycogen is the storage form of glucose in humans and other vertebrates 
and is made up of monomers of glucose. Glycogen is the animal equivalent 
of starch and is a highly branched molecule usually stored in liver and 
muscle cells. Whenever blood glucose levels decrease, glycogen is broken 
down to release glucose in a process known as glycogenolysis. 


Cellulose is the most abundant natural biopolymer. The cell wall of plants 
is mostly made of cellulose; this provides structural support to the cell. 
Wood and paper are mostly cellulosic in nature. Cellulose is made up of 
glucose monomers that are linked by f 1-4 glycosidic bonds ((link]). 


Cellulose fibers 


Cellulose structure 


H OH CH,OH H OH 
HO H H fe) H 
fe) 
OH H 
fe) 
H H H 
O lo) 
CH,OH H OH CH,OH 


In cellulose, glucose monomers are 
linked in unbranched chains by f 1-4 
glycosidic linkages. Because of the 
way the glucose subunits are joined, 
every glucose monomer is flipped 
relative to the next one resulting ina 
linear, fibrous structure. 


As shown in [link], every other glucose monomer in cellulose is flipped 
over, and the monomers are packed tightly as extended long chains. This 
gives cellulose its rigidity and high tensile strength—which is so important 
to plant cells. While the 6 1-4 linkage cannot be broken down by human 
digestive enzymes, herbivores such as cows, koalas, buffalos, and horses 
are able, with the help of the specialized flora in their stomach, to digest 
plant material that is rich in cellulose and use it as a food source. In these 
animals, certain species of bacteria and protists reside in the rumen (part of 
the digestive system of herbivores) and secrete the enzyme cellulase. The 
appendix of grazing animals also contains bacteria that digest cellulose, 
giving it an important role in the digestive systems of ruminants. Cellulases 
can break down cellulose into glucose monomers that can be used as an 
energy source by the animal. Termites are also able to break down cellulose 
because of the presence of other organisms in their bodies that secrete 
cellulases. 


Carbohydrates serve various functions in different animals. Arthropods 
(insects, crustaceans, and others) have an outer skeleton, called the 
exoskeleton, which protects their internal body parts (as seen in the bee in 
[link]). This exoskeleton is made of the biological macromolecule chitin, 
which is a polysaccharide-containing nitrogen. It is made of repeating units 
of N-acetyl-6-d-glucosamine, a modified sugar. Chitin is also a major 
component of fungal cell walls; fungi are neither animals nor plants and 
form a kingdom of their own in the domain Eukarya. 


Insects have a hard outer 
exoskeleton made of chitin, a type 
of polysaccharide. (credit: Louise 

Docker) 


Benefits of Carbohydrates 


Are carbohydrates good for you? People who wish to lose weight are often 
told that carbohydrates are bad for them and should be avoided. Some diets 
completely forbid carbohydrate consumption, claiming that a low- 
carbohydrate diet helps people to lose weight faster. However, 
carbohydrates have been an important part of the human diet for thousands 
of years; artifacts from ancient civilizations show the presence of wheat, 
rice, and corn in our ancestors’ storage areas. 


Carbohydrates should be supplemented with proteins, vitamins, and fats to 
be parts of a well-balanced diet. Calorie-wise, a gram of carbohydrate 
provides 4.3 Kcal. For comparison, fats provide 9 Kcal/g, a less desirable 
ratio. Carbohydrates contain soluble and insoluble elements; the insoluble 
part is known as fiber, which is mostly cellulose. Fiber has many uses; it 
promotes regular bowel movement by adding bulk, and it regulates the rate 
of consumption of blood glucose. Fiber also helps to remove excess 


cholesterol from the body: fiber binds to the cholesterol in the small 
intestine, then attaches to the cholesterol and prevents the cholesterol 
particles from entering the bloodstream, and then cholesterol exits the body 
via the feces. Fiber-rich diets also have a protective role in reducing the 
occurrence of colon cancer. In addition, a meal containing whole grains and 
vegetables gives a feeling of fullness. As an immediate source of energy, 
glucose is broken down during the process of cellular respiration, which 
produces ATP, the energy currency of the cell. Without the consumption of 
carbohydrates, the availability of “instant energy” would be reduced. 
Eliminating carbohydrates from the diet is not the best way to lose weight. 
A low-calorie diet that is rich in whole grains, fruits, vegetables, and lean 
meat, together with plenty of exercise and plenty of water, is the more 
sensible way to lose weight. 


Lipids 


Introduction 

"A story about the Jack Spratts of medicine [was] told recently by Dr. 
Charles H. Best, co-discoverer of insulin. He had been invited to a 
conference of heart specialists in North America. On the eve of the meeting, 
out of respect for the fat-clogs-the-arteries theory, the delegates sat down to 
a special banquet served without fats. It was unpalatable but they all ate it 
as a duty. Next morning Best looked round the breakfast room and saw 
these same specialists — all in the 40-60 year old, coronary age group — 
happily tucking into eggs, bacon, buttered toast and coffee with cream." 
Richard Mackarness, Objections To High-Fat Diets’, Eat Fat And Grow 
Slim, chapter 3, 1958 


Lipids include a diverse group of compounds, including those tasty fats in 
your diet, that are largely nonpolar in nature. This is because they are 
hydrocarbons that include mostly nonpolar carbon—carbon or carbon— 
hydrogen bonds. Non-polar molecules are hydrophobic (“water fearing”), 
or insoluble in water. Lipids perform many different functions in a cell. 
Cells store energy for long-term use in the form of fats. Lipids also provide 
insulation from the environment for plants and animals ({link]). For 
example, they help keep aquatic birds and mammals dry when forming a 
protective layer over fur or feathers because of their water-repellant 
hydrophobic nature. Lipids are also the building blocks of many hormones 
and are an important constituent of all cellular membranes. Lipids include 
fats, oils, waxes, phospholipids, and steroids. 


Hydrophobic lipids in the fur 
of aquatic mammals, such as 
this river otter, protect them 
from the elements. (credit: 
Ken Bosma) 


Fats and Oils 


A fat molecule consists of two main components—glycerol and fatty acids. 
Glycerol is an organic compound (alcohol) with three carbons, five 
hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain 
of hydrocarbons to which a carboxyl group is attached, hence the name 
“fatty acid.” The number of carbons in the fatty acid may range from 4 to 
36; most common are those containing 12—18 carbons. In a fat molecule, 
the fatty acids are attached to each of the three carbons of the glycerol 
molecule with an ester bond through an oxygen atom ((link]). 


Glycerol 


Fatty Acid 


| 


Triacylglycerol 


Triacylglycerol is formed by the joining of three 
fatty acids to a glycerol backbone in a 
condensation reaction. Three molecules of water 
are released in the process. 


During this ester bond formation, three water molecules are released. The 
three fatty acids in the triacylglycerol may be similar or dissimilar. Fats are 
also called triacylglycerols or triglycerides because of their chemical 


structure. Some fatty acids have common names that specify their origin. 
For example, palmitic acid, a saturated fatty acid, is derived from the 
palm tree. Arachidic acid is derived from Arachis hypogea, the scientific 
name for groundnuts or peanuts. 


Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there 
are only single bonds between neighboring carbons in the hydrocarbon 
chain, the fatty acid is said to be saturated. Saturated fatty acids are 
saturated with hydrogen; in other words, the number of hydrogen atoms 
attached to the carbon skeleton is maximized. Stearic acid is an example of 
a saturated fatty acid ({Llink]) 


Stearic acid is a common saturated fatty acid. 


When the hydrocarbon chain contains a double bond, the fatty acid is said 
to be unsaturated. Oleic acid is an example of an unsaturated fatty acid 


({link]). 


Oleic acid is a common unsaturated fatty acid. 


Most unsaturated fats are liquid at room temperature and are called oils. If 
there is one double bond in the molecule, then it is known as a 
monounsaturated fat (e.g., olive oil), and if there is more than one double 
bond, then it is known as a polyunsaturated fat (e.g., canola oil). 


When a fatty acid has no double bonds, it is known as a saturated fatty acid 
because no more hydrogen may be added to the carbon atoms of the chain. 
A fat may contain similar or different fatty acids attached to glycerol. Long 
straight fatty acids with single bonds tend to get packed tightly and are solid 
at room temperature. Animal fats with stearic acid and palmitic acid 
(common in meat) and the fat with butyric acid (common in butter) are 
examples of saturated fats. Mammals store fats in specialized cells called 
adipocytes, where globules of fat occupy most of the cell’s volume. In 
plants, fat or oil is stored in many seeds and is used as a source of energy 
during seedling development. Unsaturated fats or oils are usually of plant 
origin and contain cis unsaturated fatty acids. Cis and trans indicate the 
configuration of the molecule around the double bond. If hydrogens are 
present in the same plane, it is referred to as a cis fat; if the hydrogen atoms 
are on two different planes, it is referred to as a trans fat. The cis double 
bond causes a bend or a “kink” that prevents the fatty acids from packing 
tightly, keeping them liquid at room temperature ((link]). Olive oil, corn oil, 
canola oil, and cod liver oil are examples of unsaturated fats. Unsaturated 
fats help to lower blood cholesterol levels whereas saturated fats contribute 
to plaque formation in the arteries. 


Saturated fatty acid 


Stearic acid 


Unsaturated fatty acids 


Cis oleic acid 


Trans oleic acid 


Saturated fatty acids have hydrocarbon chains connected 

by single bonds only. Unsaturated fatty acids have one or 

more double bonds. Each double bond may be in a cis or 

trans configuration. In the cis configuration, both 
hydrogens are on the same side of the hydrocarbon 
chain. In the trans configuration, the hydrogens are on 
opposite sides. A cis double bond causes a kink in the 
chain. 


Trans Fats 


In the food industry, oils are artificially hydrogenated to make them semi- 
solid and of a consistency desirable for many processed food products. 
Simply speaking, hydrogen gas is bubbled through oils to solidify them. 
During this hydrogenation process, double bonds of the cis- conformation 
in the hydrocarbon chain may be converted to double bonds in the trans- 
conformation. 


Margarine, some types of peanut butter, and shortening are examples of 
artificially hydrogenated trans fats. Recent studies have shown that an 
increase in trans fats in the human diet may lead to an increase in levels of 
low-density lipoproteins (LDL), or “bad” cholesterol, which in turn may 
lead to plaque deposition in the arteries, resulting in heart disease. Many 
fast food restaurants have recently banned the use of trans fats, and food 
labels are required to display the trans fat content. 


Omega Fatty Acids 


Essential fatty acids are fatty acids required but not synthesized by the 
human body. Consequently, they have to be supplemented through ingestion 
via the diet. Omega-3 fatty acids (like that shown in [link]) fall into this 
category and are one of only two known for humans (the other being 
omega-6 fatty acid). These are polyunsaturated fatty acids and are called 
omega-3 because the third carbon from the end of the hydrocarbon chain is 
connected to its neighboring carbon by a double bond. 


Alpha-linolenic acid is an example 
of an omega-3 fatty acid. It has 
three cis double bonds and, as a 

result, a curved shape. For clarity, 
the carbons are not shown. Each 

singly bonded carbon has two 
hydrogens associated with it, also 
not shown. 


The farthest carbon away from the carboxyl group is numbered as the 
omega (@) carbon, and if the double bond is between the third and fourth 
carbon from that end, it is known as an omega-3 fatty acid. Nutritionally 
important because the body does not make them, omega-3 fatty acids 
include alpha-linoleic acid (ALA), eicosapentaenoic acid (EPA), and 
docosahexaenoic acid (DHA), all of which are polyunsaturated. Salmon, 
trout, and tuna are good sources of omega-3 fatty acids. Research indicates 
that omega-3 fatty acids reduce the risk of sudden death from heart attacks, 
reduce triglycerides in the blood, lower blood pressure, and prevent 
thrombosis by inhibiting blood clotting. They also reduce inflammation, 
and may help reduce the risk of some cancers in animals. 


Like carbohydrates, fats have received a lot of bad publicity. It is true that 
eating an excess of fried foods and other “fatty” foods leads to weight gain. 
However, fats do have important functions. Many vitamins are fat soluble, 


and fats serve as a long-term storage form of fatty acids: a source of energy. 
They also provide insulation for the body. Therefore, “healthy” fats in 
moderate amounts should be consumed on a regular basis. 


Waxes 


Wax covers the feathers of some aquatic birds and the leaf surfaces of some 
plants. Because of the hydrophobic nature of waxes, they prevent water 
from sticking on the surface ([link]). Waxes are made up of long fatty acid 
chains esterified to long-chain alcohols. 


Waxy coverings on some leaves 
are made of lipids. (credit: Roger 
Griffith) 


Phospholipids 


Phospholipids are major constituents of the plasma membrane, the 
outermost layer of animal cells. Like fats, they are composed of fatty acid 
chains attached to a glycerol or sphingosine backbone. Instead of three fatty 
acids attached as in triglycerides, however, there are two fatty acids forming 


diacylglycerol, and the third carbon of the glycerol backbone is occupied by 
a modified phosphate group ([link]). A phosphate group alone attached to a 
diaglycerol does not qualify as a phospholipid; it is phosphatidate 
(diacylglycerol 3-phosphate), the precursor of phospholipids. The 
phosphate group is modified by an alcohol. Phosphatidylcholine and 
phosphatidylserine are two important phospholipids that are found in 
plasma membranes. 


Phosphate 


Hydrophilic head 


Saturated 
fatty acid 


Unsaturated 
fatty acid 


Hydrophobic tails 


A phospholipid is a molecule with 
two fatty acids and a modified 
phosphate group attached to a 

glycerol backbone. The phosphate 

may be modified by the addition 
of charged or polar chemical 
groups. Two chemical groups that 
may modify the phosphate, 
choline and serine, are shown 
here. Both choline and serine 
attach to the phosphate group at 


the position labeled R via the 
hydroxyl group indicated in green. 


A phospholipid is an amphipathic molecule, meaning it has a hydrophobic 
and a hydrophilic part. The fatty acid chains are hydrophobic and cannot 
interact with water, whereas the phosphate-containing group is hydrophilic 
and interacts with water ((link]). 


nnngeeen Phospholipid 


bilayer 


Hydrophobic tail 


Hydrophilic head group 


The phospholipid bilayer is the 
major component of all cellular 
membranes. The hydrophilic head 
groups of the phospholipids face 
the aqueous solution. The 
hydrophobic tails are sequestered 
in the middle of the bilayer. 


The head is the hydrophilic part, and the tail contains the hydrophobic fatty 
acids. In a membrane, a bilayer of phospholipids forms the matrix of the 
structure, the fatty acid tails of phospholipids face inside, away from water, 
whereas the phosphate group faces the outside, aqueous side ([link]). 


Phospholipids are responsible for the dynamic nature of the plasma 
membrane. If a drop of phospholipids is placed in water, it spontaneously 


forms a structure known as a micelle, where the hydrophilic phosphate 
heads face the outside and the fatty acids face the interior of this structure. 


Steroids 


Unlike the phospholipids and fats discussed earlier, steroids have a fused 
ring structure. Although they do not resemble the other lipids, they are 
grouped with them because they are also hydrophobic and insoluble in 
water. All steroids have four linked carbon rings and several of them, like 
cholesterol, have a short tail (({link]). Many steroids also have the -OH 
functional group, which puts them in the alcohol classification (sterols). 


Cholesterol 


Cortisol 


Steroids such as cholesterol and 
cortisol are composed of four 
fused hydrocarbon rings. 


Cholesterol is the most common steroid. Cholesterol is mainly synthesized 
in the liver and is the precursor to many steroid hormones such as 
testosterone and estradiol, which are secreted by the gonads and endocrine 
glands. It is also the precursor to Vitamin D. Cholesterol is also the 
precursor of bile salts, which help in the emulsification of fats and their 
subsequent absorption by cells. Although cholesterol is often spoken of in 
negative terms by lay people, it is necessary for proper functioning of the 
body. It is a component of the plasma membrane of animal cells and is 
found within the phospholipid bilayer. Being the outermost structure in 
animal cells, the plasma membrane is responsible for the transport of 
materials and cellular recognition and it is involved in cell-to-cell 
communication. 


Components and Structure of Plasmal Membranes 


Introduction 

"The American Heritage Dictionary defines a membrane as a 'thin pliable 
layer of plant or animal tissue covering or separating structures or organs’. 
The impression this description leaves is one of the plastic wrap covering a 
hamburger. By this definition, membranes are static, tough, impenetrable, 
and visible. Yet, nothing could be further from the truth. The entire concept 
of dynamic behavior is missing from this definition, yet dynamics is what 
makes membranes both essential for life and so difficult to study." William 
Stillwell, An Introduction to Biological Membranes: From Bilayers to 
Rafts, pg. 1, 2013 


A cell’s plasma membrane defines the cell, outlines its borders, and 
determines the nature of its interaction with its environment. As Stillwell 
says above, without membranes there would be no life; they are as essential 
to life as DNA or proteins. Cells exclude some substances, take in others, 
and excrete still others, all in controlled quantities. The plasma membrane 
must be very flexible to allow certain cells, such as red blood cells and 
white blood cells, to change shape as they pass through narrow capillaries. 
These are the more obvious functions of a plasma membrane. In addition, 
the surface of the plasma membrane carries markers that allow cells to 
recognize one another, which is vital for tissue and organ formation during 
early development, and which later plays a role in the “self” versus “non- 
self” distinction of the immune response. 


Among the most sophisticated functions of the plasma membrane is the 
ability to transmit signals by means of complex, integral proteins known as 
membrane receptors. These proteins (and occasionally, lipids) act both as 
receivers of extracellular inputs and as activators of intracellular processes. 
These membrane receptors provide extracellular attachment sites for 
effectors like hormones and growth factors, and they activate intracellular 
response cascades when their effectors are bound. Occasionally, receptors 
are hijacked by viruses (HIV, human immunodeficiency virus, is one 
example) that use them to gain entry into cells, and at times, the genes 
encoding receptors become mutated, causing the process of signal 
transduction to malfunction with disastrous consequences. 


Fluid Mosaic Model 


The existence of the plasma membrane was identified in the 1890s, and its 
chemical components were identified in 1915. The principal components 
identified at that time were lipids and proteins. The first widely accepted 
model of the plasma membrane’s structure was proposed in 1935 by Hugh 
Davson and James Danielli; it was based on the “railroad track” appearance 
of the plasma membrane in early electron micrographs. They theorized that 
the structure of the plasma membrane resembles a sandwich, with protein 
being analogous to the bread, and lipids being analogous to the filling. In 
the 1950s, advances in microscopy, notably transmission electron 
microscopy (TEM), allowed researchers to see that the core of the plasma 
membrane consisted of a double, rather than a single, layer. A new model 
that better explains both the microscopic observations and the function of 
that plasma membrane was proposed by S.J. Singer and Garth L. Nicolson 
in 1972. 


The explanation proposed by Singer and Nicolson, and based on the work 
of many others such as Harden McConnell, is called the fluid mosaic 
model. The model has evolved somewhat over time, but it still best 
accounts for the structure and functions of the plasma membrane as we now 
understand them. The fluid mosaic model describes the structure of the 
plasma membrane as a mosaic of components—including phospholipids, 
cholesterol, proteins, and carbohydrates—that gives the membrane a fluid 
character. Plasma membranes range from 5 to 10 nm in thickness. For 
comparison, human red blood cells, visible via light microscopy, are 
approximately 8 pm wide, or approximately 1,000 times wider than a 
plasma membrane. The membrane does look a bit like a sandwich ([link]). 


Glycoprotein: protein with Glycolipid: lipid with 
[ carbohydrate attached fi carbohydrate 
attached 


Peripheral membrane Phospholipid 


protein bilayer 
Cholesterol : 
Integral membrane Protein channel 
protein 


Cytoskeletal filaments 


The fluid mosaic model of the plasma membrane describes the 
plasma membrane as a fluid combination of phospholipids, 
cholesterol, and proteins. Carbohydrates attached to lipids 
(glycolipids) and to proteins (glycoproteins) extend from the 
outward-facing surface of the membrane. 


The principal components of a plasma membrane are lipids (phospholipids 
and cholesterol), proteins, and carbohydrates attached to some of the lipids 
and some of the proteins. A phospholipid is a molecule consisting of 
glycerol, two fatty acids, and a phosphate-linked head group. Cholesterol, 
another lipid composed of four fused carbon rings, is found alongside the 
phospholipids in the core of the membrane. The proportions of proteins, 
lipids, and carbohydrates in the plasma membrane vary with cell type, but 
for a typical human cell, protein accounts for about 50 percent of the 
composition by mass, lipids (of all types) account for about 40 percent of 
the composition by mass, with the remaining 10 percent of the composition 
by mass being carbohydrates. However, the concentration of proteins and 
lipids varies with different biological membranes. For example, myelin, an 
outgrowth of the membrane of specialized cells that insulates the axons of 
the peripheral nerves, contains only 18 percent protein and 76 percent lipid. 
The mitochondrial inner membrane contains 76 percent protein and only 24 
percent lipid. The plasma membrane of human red blood cells is 30 percent 


lipid. Carbohydrates are present only on the exterior surface of the plasma 
membrane and are attached to proteins, forming glycoproteins, or attached 
to lipids, forming glycolipids. 


Phospholipids 


The main fabric of the membrane is composed of amphiphilic, phospholipid 
molecules. The hydrophilic or “water-loving” areas of these molecules 
(which look like a collection of balls in an artist’s rendition of the model) 
({link]) are in contact with the aqueous fluid both inside and outside the 
cell. Hydrophobic, or water-hating molecules, tend to be non-polar. They 
interact with other non-polar molecules in chemical reactions, but generally 
do not interact with polar molecules. When placed in water, hydrophobic 
molecules tend to form a ball or cluster. The hydrophilic regions of the 
phospholipids tend to form hydrogen bonds with water and other polar 
molecules on both the exterior and interior of the cell. Thus, the membrane 
surfaces that face the interior and exterior of the cell are hydrophilic. In 
contrast, the interior of the plasma membrane is hydrophobic and will not 
interact with water. Therefore, phospholipids form an excellent two-layer 
biological membrane that separates fluid within the cell from the fluid 
outside of the cell. 


A phospholipid molecule ([link]) consists of a three-carbon glycerol 
backbone with two fatty acid molecules attached to carbons 1 and 2, anda 
phosphate-containing group attached to the third carbon. This arrangement 
gives the overall molecule an area described as its head (the phosphate- 
containing group), which has a polar character or negative charge, and an 
area called the tail (the fatty acids), which has no charge. The head can form 
hydrogen bonds, but the tail cannot. A molecule with this arrangement of a 
positively or negatively charged area and an uncharged, or non-polar, area 
is referred to as amphiphilic or “dual-loving.” 


Phosphate 


Glycerol 


Hydrophilic head 


Saturated 
fatty acid 


Unsaturated 
fatty acid 


Hydrophobic tails 


This phospholipid molecule is 
composed of a hydrophilic head 
and two hydrophobic tails. The 

hydrophilic head group consists of 

a phosphate-containing group 
attached to a glycerol molecule. 

The hydrophobic tails, each 
containing either a saturated or an 
unsaturated fatty acid, are long 
hydrocarbon chains. 


This characteristic is vital to the structure of a plasma membrane because, 
in water, phospholipids tend to become arranged with their hydrophobic 
tails facing each other and their hydrophilic heads facing out. In this way, 
they form a lipid bilayer—a barrier composed of a double layer of 
phospholipids that separates the water and other materials on one side of the 
barrier from the water and other materials on the other side. In fact, 
phospholipids heated in an aqueous solution tend to spontaneously form 


small spheres or droplets (called micelles or liposomes), with their 
hydrophilic heads forming the exterior and their hydrophobic tails on the 
inside ([link]). 


Lipid-bilayer sphere 


Single-layer lipid sphere 


Vatatat- 
OPO 


\7 \7 \7 —-\rvvowuvoy \/ 
OOS COSC EDOCOHCOH ECHOES 


In an aqueous solution, 
phospholipids tend to arrange 
themselves with their polar heads 
facing outward and their 
hydrophobic tails facing inward. 
(credit: modification of work by 
Mariana Ruiz Villareal) 


Proteins 


Proteins make up the second major component of plasma membranes. 
Integral proteins (some specialized types are called integrins) are, as their 
name suggests, integrated completely into the membrane structure, and their 
hydrophobic membrane-spanning regions interact with the hydrophobic 
region of the the phospholipid bilayer ({link]). Single-pass integral 
membrane proteins usually have a hydrophobic transmembrane segment 
that consists of 20—25 amino acids. Some span only part of the membrane— 
associating with a single layer—while others stretch from one side of the 
membrane to the other, and are exposed on either side. Some complex 
proteins are composed of up to 12 segments of a single protein, which are 
extensively folded and embedded in the membrane ((link]). This type of 
protein has a hydrophilic region or regions, and one or several mildly 
hydrophobic regions. This arrangement of regions of the protein tends to 
orient the protein alongside the phospholipids, with the hydrophobic region 
of the protein adjacent to the tails of the phospholipids and the hydrophilic 
region or regions of the protein protruding from the membrane and in 
contact with the cytosol or extracellular fluid. 


Integral membranes proteins may 
have one or more alpha-helices that 
span the membrane (examples 1 
and 2), or they may have beta- 
sheets that span the membrane 
(example 3). (credit: 
“Foobar”/Wikimedia Commons) 


Peripheral proteins are found on the exterior and interior surfaces of 
membranes, attached either to integral proteins or to phospholipids. 
Peripheral proteins, along with integral proteins, may serve as enzymes, as 
structural attachments for the fibers of the cytoskeleton, or as part of the 
cell’s recognition sites. These are sometimes referred to as “cell-specific” 
proteins. The body recognizes its own proteins and attacks foreign proteins 
associated with invasive pathogens. 


Proteins 


Introduction 

"The characteristic specific properties of native proteins we attribute to their 
uniquely defined configurations. The denatured protein molecule we 
consider to be characterized by the absence of a uniquely defined 
configuration." Alfred E. Mirsky and Linus Pauling, "On the Structure of 
Native, Denatured and Coagulated Proteins", Proceedings of the National 
Academy of Sciences of the United States of America, 22:442-3, 1936 


Proteins are one of the most abundant organic molecules in living systems 
and have the most diverse range of functions of all macromolecules. That 
diversity of function is due to a tremendous diversity of "uniquely defined" 
structures. Proteins may be structural, regulatory, contractile, or protective; 
they may serve in transport, storage, or membranes; or they may be toxins 
or enzymes. Each cell in a living system may contain thousands of proteins, 
each with a unique function. Their structures, like their functions, vary 
greatly. They are all, however, polymers of amino acids, arranged in a linear 
sequence. But that simple linear sequence is just the beginning of the story. 


Types and Functions of Proteins 


The primary types and functions of proteins are listed in [link]. We will 
consider some of these categories in some detail, but the others will be left 
for later discussion. 


Enzymes, which are produced by living cells, are catalysts in biochemical 
reactions (like digestion) and are usually complex or conjugated proteins. 
Each enzyme is specific for the substrate (a reactant that binds to an 
enzyme) it acts on. The enzyme may help in breakdown, rearrangement, or 
synthesis reactions. Enzymes that break down their substrates are called 
catabolic enzymes, and often this is a hydrolysis reaction. Enzymes that 
build more complex molecules from their substrates are called anabolic 
enzymes, and often this is condensation reaction or dehydration synthesis. 
It should be noted that all enzymes increase the rate of reaction and, 
therefore, are considered to be organic catalysts. An example of an enzyme 
is salivary amylase, which hydrolyzes (breaks down) its substrate amylose, 


a component of starch, producing the simple disaccharide known as maltose 
along with other simpler sugars. Lastly, most but not all enzymes are 
proteins. Some enzymes are composed of RNA (Ribonucleic Acid) or have 
RNA components; a topic covered in future chapters. 


Hormones are chemical-signaling molecules, usually small proteins or 
steroids, secreted by endocrine cells that act to control or regulate specific 
physiological processes, including growth, development, metabolism, and 
reproduction. For example, insulin is a protein hormone that helps to 
regulate the blood glucose level. 


Structural proteins are some of the more familiar proteins encountered 
everyday. Hair, fingernails, and feathers are largely composed of proteins 
called keratins. Your skin contains large quantities of proteins called 
collagens and elastins. Other structural proteins are found in bone, in 
muscle, in connective tissue, etc. 


Storage proteins are used by some organisms to store energy over the long 
term, just as carbohydrates and lipids are the preferred energy storage 
molecules for other organisms. Casein, a protein found in milk, is one 
example. Zein proteins found in wheat grains provide energy for the 
developing wheat embryo, but also are critical in helping bread dough to 
rise and hold its shape. Egg albumin is an energy source for bird embryonic 
development. And proteins found in legumes, such as soybeans and other 
beans, nourish the embryos of those plants, as well as billions of humans 
around the world. 


Protein Types and Functions 


Type Examples Functions 


Protein Types and Functions 


Type 


Catabolic/Digestive 


Enzymes 


Anabolic Enzymes 


Transport 


Structural 


Hormones 


Defense 


Contractile 


Examples 


Amylase, lipase, 
pepsin, trypsin 


DNA 
polymerase, 
glycogen 
synthase 


Hemoglobin, 
albumin 


Actin, tubulin, 
keratin, collagen 


Insulin, thyroxine 


Immunoglobulins 


Actin, myosin 


Functions 


Help in digestion of 
food by catabolizing 
nutrients into 
monomers 


Enzymes that make 
polymers from 
monomers 


Carry substances in 
the blood or lymph 
throughout the body 


Compose structures 
that support cell 
organelles (e.g. 
cytoskeleton) or body 
parts (e.g. tendons, 
cartilage) 


Coordinate the 
activity of different 


body systems 


Protect the body from 
foreign pathogens 


Muscle contraction 


Protein Types and Functions 
Type Examples Functions 


Provide nourishment 

in early development 

of the embryo and the 
seedling 


Legume storage 
Storage proteins, egg 
white (albumin) 


Proteins have different shapes and molecular weights; some proteins are 
globular in shape whereas others are fibrous in nature. For example, 
hemoglobin is a globular protein, but collagen, found in our skin, is a 
fibrous protein. Protein shape is critical to its function, and this shape is 
maintained by many different types of chemical bonds. Changes in 
temperature, pH, salinity and exposure to chemicals may lead to permanent 
changes in the shape of the protein, leading to loss of function, known as 
denaturation. All proteins are made up of different arrangements of the 
same 20 types of amino acids. 


Amino Acids 


Amino acids are the monomers that make up proteins. Each amino acid has 
the same fundamental structure, which consists of a central carbon atom, 
also known as the alpha (a) carbon, bonded to an amino group (NH)), a 
carboxyl group (COOH), and to a hydrogen atom. Every amino acid also 
has another atom or group of atoms bonded to the central atom known as 
the R group ([link]). 


Amino group Carboxyl group 


a carbon 


Amino acids have a central 
asymmetric carbon to which an 
amino group, a carboxyl group, a 
hydrogen atom, and a side chain 
(R group) are attached. 


The name "amino acid" is derived from the fact that they contain both 
amino group and carboxyl-acid-group in their basic structure. As 
mentioned, there are 20 amino acids present in proteins. Ten of these are 
considered essential amino acids in humans because the human body cannot 
produce them and they are obtained from the diet. For each amino acid, the 
R group (or side chain) is different ({link]). 


Coo- 
al 
H3N—C —H 
CH, 
CH, 
Alanine ee 
] 2 


= : | 
COO NH 


Hai—¢ —H ! lees 
I *NH3 co NH» 
CH, NH, 
CH Lysine Arginine Histidine 
CHg 
CH; 
Isoleucine 


CH, 
| 
Ccoo™ 
Glutamate 
Threonine Cysteine COO- COO 
: | | | 
coo" coo- S| HN HyN—C—H H3N—C—H 
I 


- | a 
H3N—C—H  H3N—C—H 
| 


CH, 
| 
CH, 
| 
Fe 
HN No 


Proline Asparagine Glutamine 
gas Phenylalanine Tyrosine Tryptophan 


There are 20 common amino acids commonly found in 
proteins, each with a different R group (variant group) 
that determines its chemical nature. 


The chemical nature of the side chain determines the nature of the amino 
acid (that is, whether it is acidic, basic, polar, or nonpolar). For example, the 
amino acid glycine has a hydrogen atom as the R group. Amino acids such 
as valine, methionine, and alanine are nonpolar or hydrophobic in nature, 
while amino acids such as serine, threonine, and cysteine are polar and have 
hydrophilic side chains. The side chains of lysine and arginine are 
positively charged, and therefore these amino acids are also known as basic 
amino acids. Proline has an R group that is linked to the amino group, 
forming a ring-like structure. Proline is an exception to the standard 


structure of an amino acid since its amino group is not separate from the 
side chain ([link]). 


Amino acids are represented by a single upper case letter or a three-letter 
abbreviation. For example, valine is known by the letter V or the three- 
letter symbol val. Just as some fatty acids are essential to a diet, some 
amino acids are necessary as well. They are known as essential amino 

acids, and in humans they include isoleucine, leucine, and cysteine. 
Essential amino acids refer to those necessary for construction of proteins in 
the body, although not produced by the body; which amino acids are 
essential varies from organism to organism. 


The sequence and the number of amino acids ultimately determine the 
protein's shape, size, and function. Each amino acid is attached to another 
amino acid by a covalent bond, known as a peptide bond, which is formed 
by a condensation reaction. The carboxyl group of one amino acid and the 
amino group of the incoming amino acid combine, releasing a molecule of 
water. The resulting bond is the peptide bond ({link]). 


Peptide Bond 


Peptide bond formation is a 
condensation reaction. The 
carboxyl group of one amino acid 
is linked to the amino group of the 
incoming amino acid. In the 


process, a molecule of water is 
released. 


The products formed by such linkages are called peptides. As more amino 
acids join to this growing chain, the resulting chain is known as a 
polypeptide. Each polypeptide has a free amino group at one end. This end 
is called the N terminal, or the amino terminal, and the other end has a free 
carboxyl group, also known as the C or carboxy] terminal. While the terms 
polypeptide and protein are sometimes used interchangeably, a polypeptide 
is technically a polymer of amino acids, whereas the term protein is used 
for a polypeptide or polypeptides that have combined together, often have 
bound non-peptide prosthetic groups, have a distinct shape, and have a 
unique function. After protein synthesis (translation), most proteins are 
modified. These are known as post-translational modifications. They may 
undergo cleavage, phosphorylation, or may require the addition of other 
chemical groups. Only after these modifications is the protein completely 
functional. 


Note: 

Evolution Connection 

The Evolutionary Significance of Cytochrome c 

Cytochrome c is an important component of the electron transport chain, a 
part of cellular respiration, and it is normally found in the cellular 
organelle, the mitochondrion. This protein has a heme prosthetic group, 
and the central ion of the heme gets alternately reduced and oxidized 
during electron transfer. Because this essential protein’s role in producing 
cellular energy is crucial, it has changed very little over millions of years. 
Protein sequencing has shown that there is a considerable amount of 
cytochrome c amino acid sequence homology among different species; in 
other words, evolutionary kinship can be assessed by measuring the 
similarities or differences among various species’ DNA or protein 
sequences. 

Scientists have determined that human cytochrome c contains 104 amino 
acids. For each cytochrome c molecule from different organisms that has 
been sequenced to date, 37 of these amino acids appear in the same 


position in all samples of cytochrome c. This indicates that there may have 
been a common ancestor. On comparing the human and chimpanzee 
protein sequences, no sequence difference was found. When human and 
rhesus monkey sequences were compared, the single difference found was 
in one amino acid. In another comparison, human to yeast sequencing 
shows a difference in the 44th position. 


Protein Structure 


As discussed earlier, the shape of a protein is critical to its function. For 
example, an enzyme can bind to a specific substrate at a site known as the 
active site. If this active site is altered because of local changes or changes 
in overall protein structure, the enzyme may be unable to bind to the 
substrate. To understand how the protein gets its final shape or 
conformation, we need to understand the four levels of protein structure: 
primary, secondary, tertiary, and quaternary. 


Primary Structure 


The unique sequence of amino acids in a polypeptide chain is its primary 
structure. For example, the pancreatic hormone insulin has two 
polypeptide chains, A and B, and they are linked together by disulfide 
bonds. The N terminal amino acid of the A chain is glycine, whereas the C 
terminal amino acid is asparagine ({link]). The sequences of amino acids in 
the A and B chains are unique to insulin. 


Bovine serum insulin is a protein hormone made 
of two peptide chains, A (21 amino acids long) and 
B (30 amino acids long). In each chain, primary 
structure is indicated by three-letter abbreviations 
that represent the names of the amino acids in the 
order they are present. The amino acid cysteine 
(cys) has a sulfhydryl (SH) group as a side chain. 
Two sulfhydryl groups can react in the presence of 
oxygen to form a disulfide (S-S) bond. Two 
disulfide bonds connect the A and B chains 
together, and a third helps the A chain fold into the 
correct shape. Note that all disulfide bonds are the 
same length, but are drawn different sizes for 
clarity. 


The unique sequence for every protein is ultimately determined by the gene 
encoding the protein. A change in nucleotide sequence of the gene’s coding 
region may lead to a different amino acid being added to the growing 
polypeptide chain, causing a change in protein structure and function. In 
sickle cell anemia, the hemoglobin f chain (a small portion of which is 
shown in [link]) has a single amino acid substitution, causing a change in 
protein structure and function. Specifically, the amino acid glutamic acid is 
substituted by valine in the 6 chain. What is most remarkable to consider is 
that a hemoglobin molecule is made up of two alpha chains and two beta 


chains that each consist of about 150 amino acids. The molecule, therefore, 
has about 600 amino acids. The structural difference between a normal 
hemoglobin molecule and a sickle cell molecule—which dramatically 
decreases life expectancy—is a single amino acid of the 600. What is even 
more remarkable is that those 600 amino acids are encoded by three 
nucleotides each, and the mutation is caused by a single base change (point 
mutation), 1 in 1800 bases. 


H H O 
ee ee | 
threonine — proline —-N —C — O —lys 


CH, 
| ll 
CH, —C — OH 
‘ ; Normal 
glutamic acid hemoglobin 


Amino acid 
' ' 7 substitution 
threonine — proline —- N —C — 0 ——lys gy 


H3c — CH— CH 
valine Sickle cell 


hemoglobin 


The beta chain of hemoglobin is 147 
residues in length, yet a single amino 
acid substitution leads to sickle cell 
anemia. In normal hemoglobin, the 
amino acid at position seven is 
glutamate. In sickle cell hemoglobin, 
this glutamate is replaced by a valine. 


Because of this change of one amino acid in the chain, hemoglobin 
molecules form long fibers that distort the biconcave, or disc-shaped, red 
blood cells and assume a crescent or “sickle” shape, which clogs arteries 
({link]). This can lead to myriad serious health problems such as 
breathlessness, dizziness, headaches, and abdominal pain for those affected 
by this disease. 


In this blood smear, visualized at 
535x magnification using bright 
field microscopy, sickle cells are 
crescent shaped, while normal 
cells are disc-shaped. (credit: 
modification of work by Ed 
Uthman; scale-bar data from Matt 
Russell) 


Secondary Structure 


The local folding of the polypeptide in some regions gives rise to the 
secondary structure of the protein. The most common are the a-helix and 
B-pleated sheet structures ([link]). Both structure types are held in shape by 
hydrogen bonds. The hydrogen bonds form between the oxygen atom in the 
carbonyl group in one amino acid and another amino acid that is four amino 
acids farther along the chain. 


a-helix 


B-pleated 
sheet 


oO 


QomwR HoeQummR Ho HeQuemi HieQuem 1 
1 toa i) | i ie i] I 
C7ESN=C AC LN=C7ESN=C AG DN-C7ESN=C uc LN=C7ESN=C AG N-C 
eal 1 1ot I (a 1 io 
HH R HHO " Bee 6 


The a-helix and B-pleated sheet are 
secondary structures of proteins that form 
because of hydrogen bonding between 
carbonyl and amino groups in the peptide 
backbone. Certain amino acids have a 
propensity to form an a-helix, while others 
have a propensity to form a f-pleated sheet. 


Every helical turn in an alpha helix has 3.6 amino acid residues. The R 
groups (the variant groups) of the polypeptide protrude out from the a-helix 
chain. In the B-pleated sheet, the “pleats” are formed by hydrogen bonding 
between atoms on the backbone of the polypeptide chain. The R groups are 
attached to the carbons and extend above and below the folds of the pleat. 
The pleated segments align parallel or antiparallel to each other, and 
hydrogen bonds form between the partially positive nitrogen atom in the 
amino group and the partially negative oxygen atom in the carbonyl group 
of the peptide backbone. The a-helix and B-pleated sheet structures are 
found in most globular and fibrous proteins and they play an important 
structural role. 


Tertiary Structure 


The unique three-dimensional structure of a polypeptide is its tertiary 
structure ({link]). This structure is in part due to chemical interactions at 
work on the polypeptide chain. Primarily, the interactions among R groups 
creates the complex three-dimensional tertiary structure of a protein. The 
nature of the R groups found in the amino acids involved can counteract the 
formation of the hydrogen bonds described for standard secondary 
structures. For example, R groups with like charges are repelled by each 
other and those with unlike charges are attracted to each other (ionic 
bonds). When protein folding takes place, the hydrophobic R groups of 
nonpolar amino acids lay in the interior of the protein, whereas the 
hydrophilic R groups lay on the outside. The former types of interactions 
are also known as hydrophobic interactions. Interaction between cysteine 
side chains forms disulfide linkages in the presence of oxygen, the only 
covalent bond forming during protein folding. 


Polypeptide backbone 


ll 
CH, — CH, — CH, — CH, — NH3* “O—C— CH, 


lonic bond 


Dissulfide 
linkage 


Ss 
Ss 


Hydrophobic 
interactions 


The tertiary structure of proteins is determined by a 
variety of chemical interactions. These include 
hydrophobic interactions, ionic bonding, hydrogen 
bonding and disulfide linkages. 


All of these interactions, weak and strong, determine the final three- 
dimensional shape of the protein. When a protein loses its three- 
dimensional shape, it may no longer be functional. 


Quaternary Structure 


In nature, some proteins are formed from several polypeptides, also known 
as subunits, and the interaction of these subunits forms the quaternary 
structure. Weak interactions between the subunits help to stabilize the 
overall structure. For example, insulin (a globular protein) has a 
combination of hydrogen bonds and disulfide bonds that cause it to be 
mostly clumped into a ball shape. Insulin starts out as a single polypeptide 
and loses some internal sequences in the presence of post-translational 
modification after the formation of the disulfide linkages that hold the 
remaining chains together. Silk (a fibrous protein), however, has a B-pleated 
sheet structure that is the result of hydrogen bonding between different 
chains. 


The four levels of protein structure (primary, secondary, tertiary, and 
quatemary) are illustrated in [link]. 


Amino acids 
Primary Protein structure 
sequence of a chain of 
animo acids 

Pleated sheet 422 Alpha helix 

Pleated sheet Tertiary protein structure 
three-dimensional folding 
pattern of a protein due to side 
chain interactions 

Alpha helix 


g 


Quaternary protein structure 
protein consisting of more 
than one amino acid chain 


The four levels of protein structure can be 
observed in these illustrations. (credit: 
modification of work by National Human Genome 
Research Institute) 


Secondary Protein structure 


hydrogen bonding of the peptide 
backbone causes the amino 
acids to fold into a repeating 
pattern 


NAP 


Denaturation and Protein Folding 


Each protein has its own unique sequence and shape that are held together 
by chemical interactions (covalent, ionic and hydrogen bonds). As noted by 
Mirsky and Pauling in the epigraph above, a denatured protein is one that 
has lost that unique shape and configuration. If the protein is subject to 
changes in temperature, pH, salinity or exposure to chemicals, the protein 
structure may change, losing its shape without losing its primary sequence 
in what is known as denaturation. During denaturation, the changes in the 
environment surrounding the protein alter the chemical interactions (ionic 
and hydrogen bonds) within the protein causing changes in the shape and 
configuration of that protein. Denaturation may be reversible because the 
primary structure of the polypeptide is conserved in the process if the 
denaturing agent is removed, allowing the protein to resume its function. 
However, denaturation is often irreversible, leading to loss of function. One 
example of irreversible protein denaturation is when an egg is fried. The 
albumin protein in the liquid egg white is denatured when placed in a hot 
pan. Not all proteins are denatured at high temperatures; for instance, 
bacteria that survive in hot springs have proteins that function at 
temperatures close to boiling. The stomach is also very acidic, has a low 
pH, and denatures proteins as part of the digestion process; however, the 
digestive enzymes of the stomach retain their activity under these 
conditions. 


Protein folding is critical to its function. It was originally thought that the 
proteins themselves were responsible for the folding process. Only recently 
was it found that often they receive assistance in the folding process from 
protein helpers known as chaperones (or chaperonins) that associate with 
the target protein during the folding process. They act by preventing 
aggregation of polypeptides that make up the complete protein structure, 
and they disassociate from the protein once the target protein is folded. 


Enzymes 


"Yet even after Galileo and Newton, there remained another question: Were 
living things somehow different from rocks and water and stars? Did 
animate and inanimate matter differ in some fundamental way? the 
"vitalists" claimed that animate matter had some special essence, an 
intangible spirit or soul, while the "mechanists" argued that living things 
were elaborate machines and obeyed precisely the same laws of physics and 
chemistry as did inanimate material. " Alan Lightman, "Our Place in the 
Universe", Harper's Magazine, December 2012. 


One of the greatest scientists of all time, Louis Pasteur, believed that 
metabolic reactions such as fermentation could only occur in living cells. 
This perspective was widely shared by scientists of the 19th Century. Thus 
one of the first damaging blows to the vitalist perspective came in the late 
19th Century, when Eduard Buchner showed that a cell-free extract from 
yeast could carry out the synthesis of ethanol from glucose (alcoholic 
fermentation). Whole cells were not required for this process. These 
extracts were called "enzymes", which derives from the Greek words "en" 
(in) + "zyme" (yeast). Buchner demonstrated that there was something "in 
yeast", as opposed to the yeast cells themselves, that could convert glucose 
to ethanol. The subsequent work of many other scientists has built on this 
simple concept - cells contain substances that catalyze reactions, and these 
substances can be studied apart from the cells themselves. 


A substance that helps a chemical reaction to occur is a catalyst, and the 
special molecules that catalyze biochemical reactions are called enzymes. 
Almost all enzymes are proteins, made up of chains of amino acids, and 
they perform the critical task of lowering the activation energies of 
chemical reactions inside the cell. Enzymes do this by binding to the 
reactant molecules, and holding them in such a way as to make the 
chemical bond-breaking and bond-forming processes take place more 
readily. It is important to remember that enzymes don’t change the AG of a 
reaction. In other words, they don’t change whether a reaction is exergonic 
(spontaneous) or endergonic. This is because they don’t change the free 
energy of the reactants or products. They only reduce the activation energy 
required to reach the transition state ({link]). 


Activation 

energy 
Activation (Y>x) 
energy products 
(XY) 


Enzymes lower the activation 

energy of the reaction but do 

not change the free energy of 
the reaction. 


Enzyme Active Site and Substrate Specificity 


The chemical reactants to which an enzyme binds are the enzyme’s 
substrates. There may be one or more substrates, depending on the 
particular chemical reaction. In some reactions, a single-reactant substrate is 
broken down into multiple products. In others, two substrates may come 
together to create one larger molecule. Two reactants might also enter a 
reaction, both become modified, and leave the reaction as two products. 
The location within the enzyme where the substrate binds is called the 
enzyme’s active site. The active site is where the “action” happens, so to 
speak. Since enzymes are proteins, there is a unique combination of amino 
acid residues (also called side chains, or R groups) within the active site. 
Each residue is characterized by different properties. Residues can be large 
or small, weakly acidic or basic, hydrophilic or hydrophobic, positively or 
negatively charged, or neutral. The unique combination of amino acids, 
their positions, sequences, structures, and properties, creates a very specific 
chemical environment within the active site. This specific environment is 


suited to bind, albeit briefly, to a specific chemical substrate (or substrates). 
Due to this jigsaw puzzle-like match between an enzyme and its substrates 
(which adapts to find the best fit between the transition state and the active 
site), enzymes are known for their specificity. The “best fit” results from the 
shape and the amino acid functional group’s attraction to the substrate. 
There is a specifically matched enzyme for each substrate and, thus, for 
each chemical reaction; however, there is flexibility as well. 


Environmental factors influence enzyme activity 

The fact that active sites are so perfectly suited to provide specific 
environmental conditions also means that they are subject to influences by 
the local environment. The environmental conditions can include 
temperature, pH, salinity and presence of heavy metals. It is true that 
increasing the environmental temperature generally increases reaction rates, 
enzyme-catalyzed or otherwise. However, increasing or decreasing the 
temperature outside of an optimal range can affect chemical bonds within 
the active site in such a way that they are less well suited to bind substrates. 
High temperatures will eventually cause enzymes, like other biological 
molecules, to denature, a process that changes the natural properties of a 
substance. Likewise, the pH of the local environment can also affect 
enzyme function. Active site amino acids have their own acidic or basic 
properties that are optimal for catalysis. These amino acids are sensitive to 
changes in pH that can impair the way substrate molecules bind. Enzymes 
are suited to function best within a certain pH range, and, as with 
temperature, extreme pH values (acidic or basic) of the environment can 
cause enzymes to denature an the rates of the reaction decrease ([link]). 


Rate of reaction 


10 30 50 70 2 4 6 8 10 


Temperature (°C) pH 


The effects of temperature and pH on the rate 
of enzyme catalyzed reaction. 


Induced Fit and Enzyme Function 


For many years, scientists thought that enzyme-substrate binding took place 
in a simple “lock-and-key” fashion. This model asserted that the enzyme 
and substrate fit together perfectly in one instantaneous step. However, 
current research supports a more refined view called induced fit ((link]). 
The induced-fit model expands upon the lock-and-key model by describing 
a more dynamic interaction between enzyme and substrate. As the enzyme 
and substrate come together, their interaction causes a mild shift in the 
enzyme’s structure that confirms an ideal binding arrangement between the 
enzyme and the transition state of the substrate. This ideal binding 
maximizes the enzyme’s ability to catalyze its reaction. 


When an enzyme binds its substrate, an enzyme-substrate complex is 
formed. This complex lowers the activation energy of the reaction and 
promotes its rapid progression in one of many ways. On a basic level, 
enzymes promote chemical reactions that involve more than one substrate 
by bringing the substrates together in an optimal orientation. The 


appropriate region (atoms and bonds) of one molecule is juxtaposed to the 
appropriate region of the other molecule with which it must react. Another 
way in which enzymes promote the reaction of their substrates is by 
creating an optimal environment within the active site for the reaction to 
occur. Certain chemical reactions might proceed best in a slightly acidic or 
non-polar environment. The chemical properties that emerge from the 
particular arrangement of amino acid residues within an active site create 
the perfect environment for an enzyme’s specific substrates to react. 


You’ve learned that the activation energy required for many reactions 
includes the energy involved in manipulating or slightly contorting 
chemical bonds so that they can easily break and allow others to reform. 
Enzymatic action can aid this process. The enzyme-substrate complex can 
lower the activation energy by contorting substrate molecules in such a way 
as to facilitate bond-breaking, helping to reach the transition state. Finally, 
enzymes can also lower activation energies by taking part in the chemical 
reaction itself. The amino acid residues can provide certain ions or chemical 
groups that actually form covalent bonds with substrate molecules as a 
necessary step of the reaction process. In these cases, it is important to 
remember that the enzyme will always return to its original state at the 
completion of the reaction. One of the hallmark properties of enzymes is 
that they remain ultimately unchanged by the reactions they catalyze. After 
an enzyme is done catalyzing a reaction, it releases its product(s). 


Enzyme changes shape 
Substrate slightly as substrate binds 


Active site 


(2 


@ » 
y 


W, 2 


= = = 


Substrate entering Enzyme/substrate Enzyme/products Products leaving 
active site of enzyme complex complex active site of enzyme 


According to the induced-fit model, both enzyme and 
substrate undergo dynamic conformational changes upon 


binding. The enzyme contorts the substrate into its 
transition state, thereby increasing the rate of the 
reaction. 


Buffers and Enzymes 


pH and Buffers 


The pH of a solution indicates its acidity or alkalinity. The pH scale is, as 
previously mentioned, an inverse logarithm and ranges from 0 to 14 
({link]). Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and 
anything above 7.0 (from 7.1 to 14.0) is alkaline. Extremes in pH in either 
direction from 7.0 are usually considered inhospitable to life. The pH inside 
cells (6.8) and the pH in the blood (7.4) are both very close to neutral. 


13 Bleach 
12 Soapy water 
11 Ammonia solution 
10 Milk of magnesia 
9 Baking soda 
8 Sea water 
7 Distilled water 
6 Urine 
5 Black coffee 
4 Tomato juice 
3 Orange juice 
2 Lemon juice 
1 Gastric acid 
0 


The pH scale measures the 
concentration of hydrogen 
ions (H") in a solution. 
(credit: modification of work 
by Edward Stevens) 


So how can organisms whose bodies require a near-neutral pH ingest acidic 
and basic substances (a human drinking orange juice, for example) and 
survive? Buffers are the key. Buffers readily absorb excess H* or OH, 
keeping the pH of the body carefully maintained in the narrow range 
required for survival. Maintaining a constant blood pH is critical to a 
person’s well-being. The buffer maintaining the pH of human blood 
involves carbonic acid (H»CO3), bicarbonate ion (HCO3_), and carbon 
dioxide (CO2). When bicarbonate ions combine with free hydrogen ions 
and become carbonic acid, hydrogen ions are removed, moderating pH 
changes. Similarly, as shown in [link], excess carbonic acid can be 
converted to carbon dioxide gas and exhaled through the lungs. This 
prevents too many free hydrogen ions from building up in the blood and 
dangerously reducing the blood’s pH. Likewise, if too much OH™ is 
introduced into the system, carbonic acid will combine with it to create 
bicarbonate, lowering the pH. Without this buffer system, the body’s pH 
would fluctuate enough to put survival in jeopardy. 


ie HCO3__ 


This diagram shows the body’s buffering of blood pH 
levels. The blue arrows show the process of raising pH 
as more CO, is produced and exhaled. The purple 
arrows indicate the reverse process: the lowering of 
pH as more bicarbonate (HCO3_) is generated from 
the CO, being produced by cellular respiration. In 
short, when more CO, is exhaled, blood pH goes up 
and the blood is more basic, and if CO> is converted to 
bicarbonate, blood pH goes down and the blood is 
more acidic. 


Other examples of buffers are antacids used to combat excess stomach acid. 
Many of these over-the-counter medications work in the same way as blood 


buffers, usually with at least one ion capable of absorbing hydrogen and 
moderating pH, bringing relief to those that suffer “heartburn” after eating. 
The unique properties of water that contribute to this capacity to balance pH 
—as well as water’s other characteristics—are essential to sustaining life on 
Earth. 


Enzyme Function and Buffers 


On the cellular level, cells need to maintain a relatively constant internal 
environment, because many important cellular functions only take place 
within a narrow of conditions, such as temperature and pH. Enzymes 
function is influenced by the pH of its environment and only function 
optimally within a narrow pH range. Losing function of just one enzyme 
can mean death for a cell, or tissue, or organ or and entire organism. In 
addition, there are many reactions occurring in a cell that either produces or 
consumes Hydrogen ions thereby changing the pH of the cells environment. 
How do cells maintain pH within the range necessary for enzymes to 
function properly? The answer is buffers, just as learned earlier about your 
whole body using buffers to maintain its pH. 


Nucleic Acids and Nucleotides 


"If the results of the present study on the chemical nature of the 
transforming principle are confirmed, then nucleic acids must be regarded 
as possessing biological specificity, the nature of which is as yet 
undetermined." O.T. Avery, C. MacLeod, and M McCarty, "Studies on the 
Chemical Nature of the Substance Inducing Transformation of 
Pneumococcal Types", Journal of Experimental Medicine 1944, Volume 79, 
p;.155: 


In 1944, when Avery, MacLeod and McCarty published the work quoted 
above, the structure of nucleic acids was still unknown. But their work was 
one of the more important bits of evidence indicating that nucleic acids 
contained important biological information. We now know a lot more about 
the information content, and, thanks to the work of Watson and Crick a few 
years after this statement was published, we know how the structure of 
nucleic acids is related to the function of information storage, We know that 
nucleic acids are the most important macromolecules for the continuity of 
life. They carry the genetic blueprint of a cell, and carry instructions for the 
functioning of the cell. 


DNA and RNA 


The two main types of nucleic acids are deoxyribonucleic acid (DNA) and 
ribonucleic acid (RNA). DNA is the genetic material found in all living 
organisms, ranging from single-celled bacteria to multicellular mammals. It 
is found in the nucleus of eukaryotes and in the organelles, chloroplasts, and 
mitochondria. In prokaryotes, the DNA is not enclosed in a membranous 
envelope. 


The entire genetic content of a cell is known as its genome, and the study of 
genomes is genomics. In eukaryotic cells but not in prokaryotes, DNA 
forms a complex with histone proteins to form chromatin, the substance of 
eukaryotic chromosomes. A chromosome may contain tens of thousands of 
genes. Many genes contain the information to make protein products; other 
genes code for RNA products. DNA controls all of the cellular activities by 
turning the genes “on” or “off.” 


The other type of nucleic acid, RNA, is mostly involved in protein 
synthesis. The DNA molecules never leave the nucleus but instead use an 
intermediary to communicate with the rest of the cell. This intermediary is 
the messenger RNA (mRNA). Other types of RNA—like rRNA, tRNA, 
and microRNA—are involved in protein synthesis and its regulation. 


DNA and RNA are made up of monomers known as nucleotides. The 
nucleotides combine with each other to form a polynucleotide or nucleic 
acid, DNA or RNA. Each nucleotide is made up of three components: a 
nitrogenous base, a pentose (five-carbon) sugar, and a phosphate group 
({link]). Each nitrogenous base in a nucleotide is attached to a sugar 
molecule, which is attached to one or more phosphate groups. Some 
nucleotides such as ATP (Adenosine Triphosphate) are a short term energy 
source for all cells and is called the "Energy currency of the cell." 


Pyrimidines 


a or 
Ze x we 8 en 
— —- DNA) Uracil © RNA) 


Purines 


=. 
H 


rt ; 
An, af > Nn 
eA. 


Adenine AEN 


A nucleotide is made up of three components: a nitrogenous base, a 
pentose sugar, and one or more phosphate groups. Carbon residues in 
the pentose are numbered 1’ through 5’ (the prime distinguishes these 
residues from those in the base, which are numbered without using a 
prime notation). The base is attached to the 1’ position of the ribose, 
and the phosphate is attached to the 5’ position. When a 
polynucleotide is formed, the 5’ phosphate of the incoming nucleotide 
attaches to the 3’ hydroxyl group at the end of the growing chain. 
Two types of pentose are found in nucleotides, deoxyribose (found in 
DNA) and ribose (found in RNA). Deoxyribose is similar in structure 
to ribose, but it has an H instead of an OH at the 2’ position. Bases 
can be divided into two categories: purines and pyrimidines. Purines 
have a double ring structure, and pyrimidines have a single ring. 


The nitrogenous bases, important components of nucleotides, are organic 
molecules and are so named because they contain carbon and nitrogen. 
They are bases because they contain an amino group that has the potential 
of binding an extra hydrogen, and thus, decreases the hydrogen ion 
concentration in its environment, making it more basic. Each nucleotide in 
DNA contains one of four possible nitrogenous bases: adenine (A), guanine 
(G) cytosine (C), and thymine (T). 


Adenine and guanine are classified as purines. The primary structure of a 
purine is two carbon-nitrogen rings. Cytosine, thymine, and uracil are 
classified as pyrimidines which have a single carbon-nitrogen ring as their 
primary structure (({link]). Each of these basic carbon-nitrogen rings has 
different functional groups attached to it. In molecular biology shorthand, 
the nitrogenous bases are simply known by their symbols A, T, G, C, and U. 
DNA contains A, T, G, and C whereas RNA contains A, U, G, and C. 


The pentose sugar in DNA is deoxyribose, and in RNA, the sugar is ribose 
({link]). The difference between the sugars is the presence of the hydroxyl 
group on the second carbon of the ribose and hydrogen on the second 
carbon of the deoxyribose. The carbon atoms of the sugar molecule are 
numbered as 1’, 2’, 3’, 4’, and 5’ (1’ is read as “one prime”). The phosphate 


residue is attached to the hydroxyl group of the 5’ carbon of one sugar and 
the hydroxyl! group of the 3’ carbon of the sugar of the next nucleotide, 
which forms a 5'—3' phosphodiester bond. The phosphodiester bond is not 
formed by simple condensation reaction like the other linkages connecting 
monomers in macromolecules: its formation involves the removal of two 
phosphate groups. A polynucleotide may have thousands of such 
phosphodiester bonds. 


DNA Double-Helix Structure 


DNA has a double-helix structure ([link]). The sugar and phosphate lie on 
the outside of the helix, forming the backbone of the DNA. The nitrogenous 
bases are stacked in the interior, like the steps of a staircase, in pairs; the 
pairs are bound to each other by hydrogen bonds. Every base pair in the 
double helivx is separated from the next base pair by 0.34 nm. The two 
strands of the helix run in opposite directions, meaning that the 5’ carbon 
end of one strand will face the 3’ carbon end of its matching strand. (This is 
referred to as antiparallel orientation and is important to DNA replication 
and in many nucleic acid interactions.) 


Native DNA is an 
antiparallel double helix. 


The phosphate backbone 
(indicated by the curvy 
lines) is on the outside, 
and the bases are on the 
inside. Each base from 
one strand interacts via 

hydrogen bonding with a 
base from the opposing 
strand. (credit: Jerome 

Walker/Dennis Myts) 


Only certain types of base pairing are allowed. For example, a certain 
purine can only pair with a certain pyrimidine. This means A can pair with 
T, and G can pair with C, as shown in [link]. This is known as the base 
complementary rule. In other words, the DNA strands are complementary 
to each other. If the sequence of one strand is AATTGGCC, the 
complementary strand would have the sequence TTAACCGG. During 
DNA replication, each strand is copied, resulting in a daughter DNA double 
helix containing one parental DNA strand and a newly synthesized strand. 


QO Oo 
a on ~~) On 


an ----Y Cytosine fe) 
HO. Guanine NH2 vt 


In a double stranded DNA molecule, 
the two strands run antiparallel to one 
another so that one strand runs 5’ to 3’ 


and the other 3’ to 5’. The phosphate 
backbone is located on the outside, 
and the bases are in the middle. 
Adenine forms hydrogen bonds (or 
base pairs) with thymine, and guanine 
base pairs with cytosine. 


RNA 


Ribonucleic acid, or RNA, is mainly involved in the process of protein 
synthesis under the direction of DNA. RNA is usually single-stranded and 
is made of ribonucleotides that are linked by phosphodiester bonds. A 
ribonucleotide in the RNA chain contains ribose (the pentose sugar), one of 
the four nitrogenous bases (A, U, G, and C), and the phosphate group. The 
function of RNA is to make proteins from the information stored on the 
DNA. 


Features of DNA and RNA 
DNA RNA 
; Carries genetic Involved in protein 
Function ; é ’ 
information synthesis 
Location Remains in the Leaves the nucleus 
nucleus 


Structure Double helix Usually single-stranded 


Features of DNA and RNA 


DNA 
Sugar Deoxyribose 
Pyrimidines Cytosine, thymine 
Purines Adenine, guanine 


RNA 
Ribose 
Cytosine, uracil 


Adenine, guanine 


Cell Reproduction 
By the end of this section, you will be able to: 


e Describe the structure of prokaryotic and eukaryotic genomes 
e Distinguish between chromosomes, genes, and traits 
e Describe the mechanisms of chromosome compaction 


Introduction 

"DNA was the first three-dimensional Xerox machine." Kenneth E. 
Boulding, in Richard P. Beilock (ed.), Beasts, Ballads and Bouldingisms: A 
Selection of Writings by Kenneth E. Boulding, pg. 160, 1976 


Non scientists like Boulding , who was an economist, are fond of using 
machines as metaphors for biological structures and functions. But DNA is 
a lot more than just a Xerox machine, as you will learn in this section. In 
fact, the more we learn about DNA, the more remarkable it seems. For 
DNA not only replicates itself, it directs the development, life, and demise 
of every organism on the planet. 


A sea urchin 
begins life 
as a single 
cell that (a) 
divides to 

form two 
cells, visible 
by scanning 
electron 
microscopy. 
After four 
rounds of 
cell 

division, (b) 

there are 16 
cells, as 
seen in this 

SEM image. 
After many 


rounds of 
cell 
division, the 
individual 
develops 
into a 
complex, 
multicellula 
r organism, 
as seen in 
this (c) 
mature sea 
urchin. 
(credit a: 
modificatio 
n of work 
by Evelyn 
Spiegel, 
Louisa 
Howard; 
credit b: 
modificatio 
n of work 
by Evelyn 
Spiegel, 
Louisa 
Howard; 
credit c: 
modificatio 
n of work 
by Marco 
Busdraghi; 
scale-bar 
data from 
Matt 
Russell) 


A human, as well as every sexually reproducing organism, begins life as a 
fertilized egg (embryo) or zygote. Trillions of cell divisions subsequently 
occur in a controlled manner to produce a complex, multicellular human. In 
other words, that original single cell is the ancestor of every other cell in the 
body. Once a being is fully grown, cell reproduction is still necessary to 
repair or regenerate tissues. For example, new blood and skin cells are 
constantly being produced. All multicellular organisms use cell division for 
growth and the maintenance and repair of cells and tissues. Cell division is 
tightly regulated, and the occasional failure of regulation can have life- 
threatening consequences. Single-celled organisms use cell division as their 
method of reproduction. 


So, the continuity of life from one cell to another has its foundation in the 
reproduction of cells by way of the cell cycle. The cell cycle is an orderly 
sequence of events that describes the stages of a cell’s life from the division 
of a single parent cell to the production of two new daughter cells. The 
mechanisms involved in the cell cycle are highly regulated. 


Genomic DNA 


Before discussing the steps a cell must undertake to replicate, a deeper 
understanding of the structure and function of a cell’s genetic information is 
necessary. A cell’s DNA, packaged as a double-stranded DNA molecule, is 
called its genome. In prokaryotes, the genome is composed of a single, 
double-stranded DNA molecule in the form of a loop or circle ({link]). The 
region in the cell containing this genetic material is called a nucleoid. Some 
prokaryotes also have smaller loops of DNA called plasmids that are not 
essential for normal growth. Bacteria can exchange these plasmids with 


other bacteria, sometimes receiving beneficial new genes that the recipient 
can add to their chromosomal DNA. Antibiotic resistance is one trait that 
often spreads through a bacterial colony through plasmid exchange. 


Cell 
membrane 


Chromosomal DNA is 
localized in a region 
called the nucleoid. 


Prokaryotes, including bacteria 
and archaea, have a single, 
circular chromosome located in a 
central region called the nucleoid. 


In eukaryotes, the genome consists of several double-stranded linear DNA 
molecules ([link]). Each species of eukaryotes has a characteristic number 
of chromosomes in the nuclei of its cells. Human body cells have 46 
chromosomes, while human gametes (sperm or eggs) have 23 
chromosomes each. A typical body cell, or somatic cell, contains two 
matched sets of chromosomes, a configuration known as diploid. The letter 
nis used to represent a single set of chromosomes; therefore, a diploid 
organism is designated 2n. Human cells that contain one set of 
chromosomes are called gametes, or sex cells; these are eggs and sperm, 
and are designated 1n, or haploid. 


There are 23 pairs of homologous 
chromosomes in a female human 
somatic cell. The condensed 
chromosomes are viewed within 
the nucleus (top), removed from a 
cell in mitosis and spread out on a 
Slide (right), and artificially 
arranged according to length (left); 
an arrangement like this is called a 
karyotype. In this image, the 
chromosomes were exposed to 
fluorescent stains for 
differentiation of the different 
chromosomes. A method of 
staining called “chromosome 
painting” employs fluorescent 
dyes that highlight chromosomes 
in different colors. (credit: 
National Human Genome 
Project/NIH) 


Matched pairs of chromosomes in a diploid organism are called 
homologous (“same knowledge”) chromosomes. Homologous 


chromosomes are the same length and have specific nucleotide segments 
called genes in exactly the same location, or locus. Genes, the functional 
units of chromosomes, determine specific characteristics by coding for 
specific proteins. Traits are the variations of those characteristics. For 
example, hair color is a characteristic with traits that are blonde, brown, or 
black. 


Each copy of a homologous pair of chromosomes originates from a 
different parent; therefore, the genes themselves are not identical. The 
variation of individuals within a species is due to the specific combination 
of the genes inherited from both parents. Even a slightly altered sequence of 
nucleotides within a gene can result in an alternative trait. For example, 
there are three possible gene sequences on the human chromosome that 
code for blood type: sequence A, sequence B, and sequence O. Because all 
diploid human cells have two copies of the chromosome that determines 
blood type, the blood type (the trait) is determined by which two versions of 
the marker gene are inherited. It is possible to have two copies of the same 
gene sequence on both homologous chromosomes, with one on each (for 
example, AA, BB, or OO), or two different sequences, such as AB. These 
different versions of genes are called alleles. 


Minor variations of traits, such as blood type, eye color, and handedness, 
contribute to the natural variation found within a species. However, if the 
entire DNA sequence from any pair of human homologous chromosomes is 
compared, the difference is less than one percent. The sex chromosomes, X 
and Y, are the single exception to the rule of homologous chromosome 
uniformity: Other than a small amount of homology that is necessary to 
accurately produce gametes, the genes found on the X and Y chromosomes 
are different. 


Eukaryotic Chromosomal Structure and Compaction 


If the DNA from all 46 chromosomes in a human cell nucleus was laid out 
end to end, it would measure approximately two meters; however, its 
diameter would be only 2 nm. Considering that the size of a typical human 
cell is about 10 pm (100,000 cells lined up to equal one meter), DNA must 
be tightly packaged to fit in the cell’s nucleus. At the same time, it must 


also be readily accessible for the genes to be expressed. During some stages 
of the cell cycle, the long strands of DNA are condensed into compact 
chromosomes. There are a number of ways that chromosomes are 
compacted. 


In the first level of compaction, short stretches of the DNA double helix 
wrap around a core of eight histone proteins at regular intervals along the 
entire length of the chromosome ((link]). The DNA-histone complex is 
called chromatin. The beadlike, histone DNA complex is called a 
nucleosome, and DNA connecting the nucleosomes is called linker DNA. A 
DNA molecule in this form is about seven times shorter than the double 
helix without the histones, and the beads are about 10 nm in diameter, in 
contrast with the 2-nm diameter of a DNA double helix. The next level of 
compaction occurs as the nucleosomes and the linker DNA between them 
are coiled into a 30-nm chromatin fiber. This coiling further shortens the 
chromosome so that it is now about 50 times shorter than the extended 
form. In the third level of packing, a variety of fibrous proteins is used to 
pack the chromatin. These fibrous proteins also ensure that each 
chromosome in a non-dividing cell occupies a particular area of the nucleus 
that does not overlap with that of any other chromosome (see the top image 
in [link)). 


Organization of Eukaryotic Chromosomes 


DNA double 
helix 


DNA wrapped 
around histone 


Nucleosomes 
coiled into a 
chromatin 
fiber 


Further 
condensation 
of chromatin 


Duplicated 
chromosome 


Double-stranded DNA wraps 
around histone proteins to form 
nucleosomes that have the 
appearance of “beads on a string.” 
The nucleosomes are coiled into a 
30-nm chromatin fiber. When a 
cell undergoes mitosis, the 
chromosomes condense even 
further. 


DNA replicates in the S phase of interphase. After replication, the 
chromosomes are composed of two linked sister chromatids. When fully 


compact, the pairs of identically packed chromosomes are bound to each 
other by cohesin proteins. The connection between the sister chromatids is 
closest in a region called the centromere. The conjoined sister chromatids, 
with a diameter of about 1 jm, are visible under a light microscope. The 
centromeric region is highly condensed and thus will appear as a constricted 
area. 


DNA Replication 
By the end of this section, you will be able to: 


e Explain the process of DNA replication 
e Explain the importance of telomerase to DNA replication 
e Describe mechanisms of DNA repair 


When a cell divides, it is important that each daughter cell receives an 
identical copy of the DNA. This is accomplished by the process of DNA 
replication. The replication of DNA occurs during the synthesis phase, or S 
phase, of the cell cycle, before the cell enters mitosis or meiosis. 


The elucidation of the structure of the double helix provided a hint as to 
how DNA is copied. Recall that adenine nucleotides pair with thymine 
nucleotides, and cytosine with guanine. This means that the two strands are 
complementary to each other. For example, a strand of DNA witha 
nucleotide sequence of AGTCATGA will have a complementary strand 
with the sequence TCAGTACT ((link]). 

3! 


LL LR) De 
ee a ie ie a ee 


ai 


The two strands of DNA are 
complementary, meaning the sequence of 
bases in one strand can be used to create the 
correct sequence of bases in the other strand. 


Because of the complementarity of the two strands, having one strand 
means that it is possible to recreate the other strand. This model for 
replication suggests that the two strands of the double helix separate during 
replication, and each strand serves as a template from which the new 
complementary strand is copied ((Link]). 


Semi-conservative model of DNA Replication 


The semiconservative model of 
DNA replication is shown. Gray 
indicates the original DNA 
strands, and blue indicates newly 
synthesized DNA. 


During DNA replication, each of the two strands that make up the double 
helix serves as a template from which new strands are copied. The new 
strand will be complementary to the parental or “old” strand. Each new 
double strand consists of one parental strand and one new daughter strand. 
This is known as semiconservative replication. When two DNA copies are 
formed, they have an identical sequence of nucleotide bases and are divided 
equally into two daughter cells. 


DNA Replication in Eukaryotes 


Because eukaryotic genomes are very complex, DNA replication is a very 
complicated process that involves several enzymes and other proteins. It 
occurs in three main stages: initiation, elongation, and termination. 


Recall that eukaryotic DNA is bound to proteins known as histones to form 
structures called nucleosomes. During initiation, the DNA is made 
accessible to the proteins and enzymes involved in the replication process. 
How does the replication machinery know where on the DNA double helix 
to begin? It turns out that there are specific nucleotide sequences called 
origins of replication at which replication begins. Certain proteins bind to 
the origin of replication while an enzyme called helicase unwinds and 
opens up the DNA helix. As the DNA opens up, Y-shaped structures called 
replication forks are formed ((link]). Two replication forks are formed at 
the origin of replication, and these get extended in both directions as 
replication proceeds. There are multiple origins of replication on the 
eukaryotic chromosome, such that replication can occur simultaneously 
from several places in the genome. 


During elongation, an enzyme called DNA polymerase adds DNA 
nucleotides to the 3' end of the template. Because DNA polymerase can 
only add new nucleotides at the end of a backbone, a primer sequence, 
which provides this starting point, is added with complementary RNA 
nucleotides. This primer is removed later, and the nucleotides are replaced 
with DNA nucleotides. One strand, which is complementary to the parental 
DNA strand, is synthesized continuously toward the replication fork so the 
polymerase can add nucleotides in this direction. This continuously 
synthesized strand is known as the leading strand. Because DNA 


polymerase can only synthesize DNA ina 5' to 3' direction, the other new 
strand is put together in short pieces called Okazaki fragments. The 
Okazaki fragments each require a primer made of RNA to start the 
synthesis. The strand with the Okazaki fragments is known as the lagging 
strand. As synthesis proceeds, an enzyme removes the RNA primer, which 
is then replaced with DNA nucleotides, and the gaps between fragments are 
sealed by an enzyme called DNA ligase. 


The process of DNA replication can be summarized as follows: 


1. DNA unwinds at the origin of replication. 

2. New bases are added to the complementary parental strands. One new 
strand is made continuously, while the other strand is made in pieces. 

3. Primers are removed, new DNA nucleotides are put in place of the 
primers and the backbone is sealed by DNA ligase. 


Helicase 


<q” 
3 XY 5' 3 5! 3] 5 
Lagging 
strand 


RNA Okazaki Leading Newly made DNA 
primer fragment strand DNA strands polymerase 


A replication fork is formed by the opening of the 
origin of replication, and helicase separates the 
DNA strands. An RNA primer is synthesized, and 
is elongated by the DNA polymerase. On the 
leading strand, DNA is synthesized continuously, 
whereas on the lagging strand, DNA is synthesized 
in short stretches. The DNA fragments are joined 
by DNA ligase (not shown). 


Telomere Replication 


Because eukaryotic chromosomes are linear, DNA replication comes to the 
end of a line in eukaryotic chromosomes. As you have learned, the DNA 
polymerase enzyme can add nucleotides in only one direction. In the 
leading strand, synthesis continues until the end of the chromosome is 
reached; however, on the lagging strand there is no place for a primer to be 
made for the DNA fragment to be copied at the end of the chromosome. 
This presents a problem for the cell because the ends remain unpaired, and 
over time these ends get progressively shorter as cells continue to divide. 
The ends of the linear chromosomes are known as telomeres, which have 
repetitive sequences that do not code for a particular gene. As a 
consequence, it is telomeres that are shortened with each round of DNA 
replication instead of genes. For example, in humans, a six base-pair 
sequence, TTAGGG, is repeated 100 to 1000 times. The discovery of the 
enzyme telomerase ((link]) helped in the understanding of how 
chromosome ends are maintained. The telomerase attaches to the end of the 
chromosome, and complementary bases to the RNA template are added on 
the end of the DNA strand. Once the lagging strand template is sufficiently 
elongated, DNA polymerase can now add nucleotides that are 
complementary to the ends of the chromosomes. Thus, the ends of the 
chromosomes are replicated. 


, , 


hg pW ea et a a a ft 
CCATGCATTGGTTAG 


GGTAC 
9 decked 5’ CAAUCCCAAUC 
telomerase 


Telomerase has an associated RNA that complements 
the 3’ overhang at the end of the chromosome. 


SS a se ee 
CCATGCATTGGTTAGGGTTAG 


,GGTAC , GAAUGGCGAAUC 
2 dendentenionts 5 telomerase 


The RNA template is used to synthesize the complementary 
strand. J 


0 oe Co en 
CCATGCATTGGTTAGGGTTAG 

GET Ae. CAAUCCCAAUC 

2! detentions 5 telomerase 


Telomerase shifts, and the process is repeated. 


} 


, a 


SS eS OO ee 
CCATGCATTGGTTAGGGTTAGGGTTAG 


GGTAC AATCCCAAT 
3’ hedecledels 5’ 7 ee oe 
Primase and DNA polymerase synthesize the complementary 
strand. 


The ends of linear chromosomes are 
maintained by the action of the 
telomerase enzyme. 


Telomerase is typically found to be active in germ cells, adult stem cells, 
and some cancer cells. For her discovery of telomerase and its action, 
Elizabeth Blackburn ([link]) received the Nobel Prize for Medicine and 
Physiology in 2009. 


Elizabeth Blackburn, 2009 Nobel 
Laureate, was the scientist who 
discovered how telomerase works. 
(credit: U.S. Embassy, Stockholm, 
Sweden) 


Telomerase is not active in adult somatic cells. Adult somatic cells that 
undergo cell division continue to have their telomeres shortened. This 
essentially means that telomere shortening is associated with aging. In 
2010, scientists found that telomerase can reverse some age-related 
conditions in mice, and this may have potential in regenerative medicine. 
[footnote] Te]gmerase-deficient mice were used in these studies; these mice 
have tissue atrophy, stem-cell depletion, organ system failure, and impaired 
tissue injury responses. Telomerase reactivation in these mice caused 
extension of telomeres, reduced DNA damage, reversed neurodegeneration, 
and improved functioning of the testes, spleen, and intestines. Thus, 
telomere reactivation may have potential for treating age-related diseases in 
humans. 

Mariella Jaskelioff, et al., “Telomerase reactivation reverses tissue 
degeneration in aged telomerase-deficient mice,” Nature, 469 (2011):102-—7. 


DNA Repair 


DNA polymerase can make mistakes while adding nucleotides. It edits the 
DNA by proofreading every newly added base. Incorrect bases are removed 
and replaced by the correct base, and then polymerization continues 
({link]a). Most mistakes are corrected during replication, although when 
this does not happen, the mismatch repair mechanism is employed. 
Mismatch repair enzymes recognize the wrongly incorporated base and 
excise it from the DNA, replacing it with the correct base ({link]|b). In yet 
another type of repair, nucleotide excision repair, the DNA double strand is 
unwound and separated, the incorrect bases are removed along with a few 
bases on the 5' and 3' end, and these are replaced by copying the template 
with the help of DNA polymerase ((link]c). Nucleotide excision repair is 
particularly important in correcting thymine dimers, which are primarily 
caused by ultraviolet light. In a thymine dimer, two thymine nucleotides 
adjacent to each other on one strand are covalently bonded to each other 
rather than their complementary bases. If the dimer is not removed and 
repaired it will lead to a mutation. Individuals with flaws in their nucleotide 
excision repair genes show extreme sensitivity to sunlight and develop skin 
cancers early in life. 


3’ 
G 
GGTTAGCCGATTCA 


eekek lll A 
lhl le aie lh lon 


DNA polymerase 


(a) Proofreading 


(c) Nucleotide Excision 


Proofreading by DNA polymerase 
(a) corrects errors during 
replication. In mismatch repair (b), 


the incorrectly added base is 
detected after replication. The 
mismatch repair proteins detect 
this base and remove it from the 
newly synthesized strand by 
nuclease action. The gap is now 
filled with the correctly paired 
base. Nucleotide excision (c) 
repairs thymine dimers. When 
exposed to UV, thymines lying 
adjacent to each other can form 
thymine dimers. In normal cells, 
they are excised and replaced. 


Most mistakes are corrected; if they are not, they may result in a mutation 
—defined as a permanent change in the DNA sequence. Mutations in repair 


genes may lead to serious consequences like cancer. 


Prokaryotic Cell Division 


Introduction 

",..(T)he extreme rapidity with which generation succeeds generation 
amongst bacteria offers to the forces of variation and natural selection a field 
for their operation wholly unparalleled amongst higher forms of life." 
Frederick W. Andrewes, "The Evolution of the Streptococci", The Lancet, 
2:1415, 1906 


Prokaryotes such as bacteria propagate by binary fission, and produces two 
identical daughter cells. This is a simpler process than cell division in 
eukaryotes, partly because there is no need for separate nuclear and cellular 
divisions (mitosis and cytokinesis, respectively). As Andrewes noted, the 
rapidity of cell reproduction in prokaryotes opens the door for rapid 
evolutionary change in these organisms. 


To achieve the outcome of identical daughter cells, some steps are essential. 
The genomic DNA must be replicated and then allocated into the daughter 
cells; the cytoplasmic contents must also be divided to give both new cells 
the machinery to sustain life. In bacterial cells, the genome consists of a 
single, circular DNA chromosome; therefore, the process of cell division is 
simplified. Mitosis is unnecessary because there is no nucleus or multiple 
chromosomes. This type of cell division is called binary fission. 


Binary Fission 


The cell division process of prokaryotes, called binary fission, is a less 
complicated and much quicker process than cell division in eukaryotes. 
Because of the speed of bacterial cell division, populations of bacteria can 
grow very rapidly. The single, circular DNA chromosome of bacteria is not 
enclosed in a nucleus, but instead occupies a specific location, the nucleoid, 
within the cell. As in eukaryotes, the DNA of the nucleoid is associated with 
proteins that aid in packaging the molecule into a compact size. The packing 
proteins of bacteria are, however, related to some of the proteins involved in 
the chromosome compaction of eukaryotes. 


The starting point of replication, the origin, is close to the binding site of the 
chromosome to the plasma membrane ([link]). Replication of the DNA is 


bidirectional—moving away from the origin on both strands of the DNA 
loop simultaneously. As the new double strands are formed, each origin point 
moves away from the cell-wall attachment toward opposite ends of the cell. 
As the cell elongates, the growing membrane aids in the transport of the 
chromosomes. After the chromosomes have cleared the midpoint of the 
elongated cell, cytoplasmic separation begins. A septum is formed between 
the nucleoids from the periphery toward the center of the cell. When the new 
cell walls are in place, the daughter cells separate. 


Replication of the circular prokaryotic chromosome begins at the origin of replication 
and continues in both directions at once. 


Origin of replication 


Prokaryotes have a single, 
circular chromosome 


FtsZ protein 


The cell begins to elongate. FtsZ proteins migrate toward the midpoint of the cell. 


The duplicated chromosomes separate and continue to move away from each other 
toward opposite ends of the cell. FtsZ proteins form a ring around the periphery of the 
midpoint between the chromosomes. 


Cleavage furrow 
FtsZ ring 


The FtsZ ring directs the formation of a septum that divides the cell. Plasma membrane 
and cell wall materials accumulate. 


Septum 


After the septum is complete, the cell pinches in two, forming two daughter cells. FtsZ is 
dispersed throughout the cytoplasm of the new cells. 


The binary fission of a bacterium is outlined in 
five steps. (credit: modification of work by 
“Mcstrother”/Wikimedia Commons) 


Note: 


Evolution in Action 

Mitotic Spindle Apparatus 

The precise timing and formation of the mitotic spindle is critical to the 
success of eukaryotic cell division. Prokaryotic cells, on the other hand, do 
not undergo mitosis and therefore have no need for a mitotic spindle. 
However, the FtsZ protein that plays such a vital role in prokaryotic 
cytokinesis is structurally and functionally very similar to tubulin, the 
building block of the microtubules that make up the mitotic spindle fibers 
that are necessary for eukaryotes. The formation of a ring composed of 
repeating units of a protein called FtsZ directs the partition between the 
nucleoids in prokaryotes. Formation of the FtsZ ring triggers the 
accumulation of other proteins that work together to recruit new membrane 
and cell-wall materials to the site. FtsZ proteins can form filaments, rings, 
and other three-dimensional structures resembling the way tubulin forms 
microtubules, centrioles, and various cytoskeleton components. In addition, 
both FtsZ and tubulin employ the same energy source, GTP (guanosine 
triphosphate), to rapidly assemble and disassemble complex structures. 
FtsZ and tubulin are an example of homology, structures derived from the 
same evolutionary origins. In this example, FtsZ is presumed to be similar 
to the ancestor protein to both the modern FtsZ and tubulin. While both 
proteins are found in extant organisms, tubulin function has evolved and 
diversified tremendously since the evolution from its FtsZ-like prokaryotic 
origin. A survey of cell-division machinery in present-day unicellular 
eukaryotes reveals crucial intermediary steps to the complex mitotic 
machinery of multicellular eukaryotes ([link]). 


Mitotic Spindle Evolution 


Structure of Division of 
genetic nuclear Separation of 
material material daughter cells 


Mitotic Spindle Evolution 


Prokaryotes 


Some 
protists 


Structure of 
genetic 
material 


There is no 
nucleus. The 
single, 
circular 
chromosome 
exists ina 
region of 
cytoplasm 
called the 
nucleoid. 


Linear 
chromosomes 
exist in the 
nucleus. 


Division of 
nuclear 
material 


Occurs 
through 
binary fission. 
As the 
chromosome 
is replicated, 
the two copies 
move to 
opposite ends 
of the cell by 
an unknown 
mechanism. 


Chromosomes 
attach to the 
nuclear 
envelope, 
which 
remains 
intact. The 
mitotic 
spindle passes 
through the 
envelope and 
elongates the 
cell. No 
centrioles 
exist. 


Separation of 
daughter cells 


FtsZ proteins 
assemble into a 
ring that 
pinches the 
cell in two. 


Microfilaments 
form a 
cleavage 
furrow that 
pinches the 
cell in two. 


Mitotic Spindle Evolution 


Structure of 
genetic 
material 


Linear 
chromosomes 
exist in the 
nucleus. 


Other 
protists 


Division of 
nuclear 
material 


Separation of 
daughter cells 


A mitotic 
spindle forms 
from the 
centrioles and 
passes 
through the 
nuclear 
membrane, 
which 
remains 
intact. 
Chromosomes 
attach to the 
mitotic 
spindle. The 
mitotic 
spindle 
separates the 
chromosomes 
and elongates 
the cell. 


Microfilaments 
form a 
cleavage 
furrow that 
pinches the 
cell in two. 


Mitotic Spindle Evolution 


Structure of 


Division of 


genetic nuclear Separation of 
material material daughter cells 
A mitotic 
spindle forms 
from the 
centrioles. 
The nuclear 
envelope Microfilaments 
Linear dissolves. form a 
Animal chromosomes Chromosomes cleavage 
cells exist in the attach to the furrow that 
nucleus. mitotic pinches the 
spindle, cell in two. 
which 
separates 
them and 


elongates the 
cell. 


The mitotic spindle fibers of eukaryotes are composed of microtubules. 
Microtubules are polymers of the protein tubulin. The FtsZ protein active in 
prokaryote cell division is very similar to tubulin in the structures it can form 
and its energy source. Single-celled eukaryotes (such as yeast) display 
possible intermediary steps between FtsZ activity during binary fission in 
prokaryotes and the mitotic spindle in multicellular eukaryotes, during which 
the nucleus breaks down and is reformed. 


Eukaryotic Cell Cycle 


Introduction 

"These facts show that mitosis is due to the coordinate play of an extremely 
complex system of forces which are as yet scarcely comprehended." 
Edmund B. Wilson, The Cell in Development and Inheritance, pg. 86, 1896 


Wilson was correct in regarding mitosis and cell division as being 
"extremely complex". But in the century or so that has passed since he 
wrote those words, we have learned quite a lot about the nature of that 
complexity. The process has even been given a name: the cell cycle. The 
cell cycle is an ordered series of events involving cell growth and cell 
division that produces two new daughter cells. Cells on the path to cell 
division proceed through a series of precisely timed and carefully regulated 
stages of growth, DNA replication, and division that produce two 
genetically identical cells. The cell cycle has two major phases: interphase 
and the mitotic phase ([link]). During interphase, the cell grows and DNA 
is replicated. During the mitotic phase, the replicated DNA and 


cytoplasmic contents are separated and the cell divides. 
Mitotic Phase 


Interphase 
Mitosis Formation 
Cytokinesis ti caLginer 


Ils 


Interphase Interphase 


A cell moves through a series of phases in an orderly 
manner. During interphase, G, involves cell growth and 


protein synthesis, the S phase involves DNA replication 
and the replication of the centrosome, and G> involves 

further growth and protein synthesis. The mitotic phase 
follows interphase. Mitosis is nuclear division during 

which duplicated chromosomes are segregated and 
distributed into daughter nuclei. Usually the cell will 
divide after mitosis in a process called cytokinesis in 
which the cytoplasm is divided and two daughter cells 
are formed. 


Interphase 


During interphase, the cell undergoes normal processes while also preparing 
for cell division. For a cell to move from interphase to the mitotic phase, 
many internal and external conditions must be met. The three stages of 
interphase are called G,, S, and Gp. 


G, Phase 


The first stage of interphase is called the G, phase, or first gap, because 
little change is visible under the microscope. However, during the G, stage, 
the cell is quite active at the biochemical level. The cell is accumulating the 
building blocks of chromosomal DNA and the associated proteins, as well 
as accumulating enough energy reserves to complete the task of replicating 
each chromosome in the nucleus. 


S Phase 


Throughout interphase, nuclear DNA remains in a semi-condensed 

chromatin configuration. In the S phase (synthesis phase), DNA replication 
results in the formation of two identical copies of each chromosome—sister 
chromatids—that are firmly attached at the centromere region. At this stage, 


each chromosome is made of two sister chromatids and is a duplicated 
chromosome. The centrosome is duplicated during the S phase. The two 
centrosomes will give rise to the mitotic spindle, the apparatus that 
orchestrates the movement of chromosomes during mitosis. The centrosome 
consists of a pair of rod-like centrioles at right angles to each other. 
Centrioles help organize cell division. Centrioles are not present in the 
centrosomes of many eukaryotic species, such as plants and most fungi. 


G> Phase 


In the Gp phase, or second gap, the cell replenishes its energy stores and 
synthesizes the proteins necessary for chromosome manipulation. Some cell 
organelles are duplicated, and the cytoskeleton is partially dismantled to 
provide building blocks for the mitotic spindle. There may be additional 
cell growth during G>. The final preparations for the mitotic phase must be 
completed before the cell is able to enter the first stage of mitosis. 


The Mitotic Phase 


To make two daughter cells, the contents of the nucleus and the cytoplasm 
must be divided. The mitotic phase is a multistep process during which the 
duplicated chromosomes are aligned, separated, and moved to opposite 
poles of the cell, and then the cell is divided into two new identical daughter 
cells. The first portion of the mitotic phase, mitosis, is composed of five 
stages, which accomplish nuclear division. The second portion of the 
mitotic phase, called cytokinesis, is the physical separation of the 
cytoplasmic components into two daughter cells. 


Mitosis 


Mitosis is divided into a series of phases—prophase, metaphase, anaphase, 
and telophase—that result in the division of the cell nucleus (({Llink]). 


* Chromosomes 
condense and 
become visible 


* Spindle fibers 
emerge from the 
centrosomes 


* Nuclear envelope 
breaks down 


+ Centrosomes 
move toward 
opposite poles 


are lined up at 
the metaphase 
plate 


Each sister 
chromatid is 
attached to a 
spindle fiber 
originating from 
opposite poles 


MITOSIS 


« Centromeres 
split in two 


are pulled toward surrounds 
opposite poles each set of 
chromosomes 
* Certain spindle 
fibers begin to * The mitotic 
elongate the cell spindle breaks 
down 


* Spindle fibers 
continue to push 
poles apart 


cleavage furrow 
separates the 
daughter cells 


* Plant cells: a cell 
precursor toa 
new cell wall, 
separates the 
daughter cells 


Animal cell mitosis is divided into four stages—prophase, metaphase, 
anaphase, and telophase—visualized here by light microscopy with 
fluorescence. Mitosis is usually accompanied by cytokinesis, shown 

here by a transmission electron microscope. (credit "diagrams": 

modification of work by Mariana Ruiz Villareal; credit "mitosis 
micrographs": modification of work by Roy van Heesbeen; credit 
"cytokinesis micrograph": modification of work by the Wadsworth 
Center, NY State Department of Health; donated to the Wikimedia 


foundation; scale-bar data from Matt Russell) 


During prophase, the “first phase,” several events must occur to provide 
access to the chromosomes in the nucleus. The nuclear envelope starts to 
break into small vesicles, and the Golgi apparatus and endoplasmic 
reticulum fragment and disperse to the periphery of the cell. The nucleolus 


disappears. The centrosomes begin to move to opposite poles of the cell. 
The microtubules that form the basis of the mitotic spindle extend between 
the centrosomes, pushing them farther apart as the microtubule fibers 
lengthen. The sister chromatids begin to coil more tightly and become 
visible under a light microscope. Also, each sister chromatid attaches to 
spindle microtubules at the centromere via a protein complex called the 
kinetochore. 


During metaphase, all of the chromosomes are aligned in a plane called the 
metaphase plate, or the equatorial plane, midway between the two poles of 
the cell. The sister chromatids are still tightly attached to each other. At this 
time, the chromosomes are maximally condensed. 


During anaphase, the sister chromatids at the equatorial plane are split 
apart at the centromere. Each chromatid, now called a chromosome, is 
pulled rapidly toward the centrosome to which its microtubule was 
attached. The cell becomes visibly elongated as the non-kinetochore 
microtubules slide against each other at the metaphase plate where they 
overlap. 


During telophase, all of the events that set up the duplicated chromosomes 
for mitosis during the first three phases are reversed. The chromosomes 
reach the opposite poles and begin to decondense (unravel). The mitotic 
spindles are broken down into monomers that will be used to assemble 
cytoskeleton components for each daughter cell. Nuclear envelopes form 
around chromosomes. 


Cytokinesis 


Cytokinesis is the second part of the mitotic phase during which cell 
division is completed by the physical separation of the cytoplasmic 
components into two daughter cells. Although the stages of mitosis are 
similar for most eukaryotes, the process of cytokinesis is quite different for 
eukaryotes that have cell walls, such as plant cells. 


In cells such as animal cells that lack cell walls, cytokinesis begins 
following the onset of anaphase. A contractile ring composed of actin 
filaments forms just inside the plasma membrane at the former metaphase 
plate. The actin filaments pull the equator of the cell inward, forming a 
fissure. This fissure, or “crack,” is called the cleavage furrow. The furrow 
deepens as the actin ring contracts, and eventually the membrane and cell 
are cleaved in two ([link]). 


In plant cells, a cleavage furrow is not possible because of the rigid cell 
walls surrounding the plasma membrane. A new cell wall must form 
between the daughter cells. During interphase, the Golgi apparatus 
accumulates enzymes, structural proteins, and glucose molecules prior to 
breaking up into vesicles and dispersing throughout the dividing cell. 
During telophase, these Golgi vesicles move on microtubules to collect at 
the metaphase plate. There, the vesicles fuse from the center toward the cell 
walls; this structure is called a cell plate. As more vesicles fuse, the cell 
plate enlarges until it merges with the cell wall at the periphery of the cell. 
Enzymes use the glucose that has accumulated between the membrane 
layers to build a new cell wall of cellulose. The Golgi membranes become 
the plasma membrane on either side of the new cell wall ({link]). 


(a) Animal cell 


Cleavage 

furrow E> 

Contractile 

ring 

Cell 

8 ~ 


Golgi vesicles 


(b) Plant cell 


In part (a), a cleavage furrow forms at 
the former metaphase plate in the 
animal cell. The plasma membrane is 
drawn in by a ring of actin fibers 
contracting just inside the membrane. 
The cleavage furrow deepens until the 
cells are pinched in two. In part (b), 
Golgi vesicles coalesce at the former 
metaphase plate in a plant cell. The 
vesicles fuse and form the cell plate. 
The cell plate grows from the center 
toward the cell walls. New cell walls 
are made from the vesicle contents. 


G, Phase 


Not all cells adhere to the classic cell-cycle pattern in which a newly 
formed daughter cell immediately enters interphase, closely followed by the 


mitotic phase. Cells in the Gp phase are not actively preparing to divide. 
The cell is in a quiescent (inactive) stage, having exited the cell cycle. Some 
cells enter Gg temporarily until an external signal triggers the onset of G,. 
Other cells that never or rarely divide, such as mature cardiac muscle and 
nerve cells, remain in Gp permanently ((link]). 


Gy 
Cells not 


actively 
dividing 


Cell Cycle 


Cells that are not actively 
preparing to divide enter an 
alternate phase called Go. In some 
cases, this is a temporary 
condition until triggered to enter 
G,. In other cases, the cell will 
remain in Gp permanently. 


Control of the Cell Cycle 


The length of the cell cycle is highly variable even within the cells of an 
individual organism. In humans, the frequency of cell turnover ranges from 
a few hours in early embryonic development to an average of two to five 


days for epithelial cells, or to an entire human lifetime spent in Gp by 
specialized cells such as cortical neurons or cardiac muscle cells. There is 
also variation in the time that a cell spends in each phase of the cell cycle. 
When fast-dividing mammalian cells are grown in culture (outside the body 
under optimal growing conditions), the length of the cycle is approximately 
24 hours. In rapidly dividing human cells with a 24-hour cell cycle, the G; 
phase lasts approximately 11 hours. The timing of events in the cell cycle is 
controlled by mechanisms that are both internal and external to the cell. 


Regulation at Internal Checkpoints 


It is essential that daughter cells be exact duplicates of the parent cell. 
Mistakes in the duplication or distribution of the chromosomes lead to 
mutations that may be passed forward to every new cell produced from the 
abnormal cell. To prevent a compromised cell from continuing to divide, 
there are internal control mechanisms that operate at three main cell cycle 
checkpoints at which the cell cycle can be stopped until conditions are 
favorable. These checkpoints occur near the end of Gj, at the G>-M 
transition, and during metaphase ((link]). 


Mitotic Phase 


G, Checkpoint 
M Checkpoint Formation 
of 2 daughter 


cells 


G, Checkpoint 
(restriction) 


The cell cycle is controlled at three checkpoints. 
Integrity of the DNA is assessed at the G; 
checkpoint. Proper chromosome duplication is 
assessed at the G» checkpoint. Attachment of each 
kinetochore to a spindle fiber is assessed at the M 
checkpoint. 


The G, Checkpoint 


The G, checkpoint determines whether all conditions are favorable for cell 
division to proceed. The G, checkpoint, also called the restriction point, is 
the point at which the cell irreversibly commits to the cell-division process. 
In addition to adequate reserves and cell size, there is a check for damage to 
the genomic DNA at the G, checkpoint. A cell that does not meet all the 
requirements will not be released into the S phase. 


The Gy Checkpoint 


The G> checkpoint bars the entry to the mitotic phase if certain conditions 
are not met. As in the G, checkpoint, cell size and protein reserves are 
assessed. However, the most important role of the G» checkpoint is to 
ensure that all of the chromosomes have been replicated and that the 
replicated DNA is not damaged. 


The M Checkpoint 


The M checkpoint occurs near the end of the metaphase stage of mitosis. 
The M checkpoint is also known as the spindle checkpoint because it 
determines if all the sister chromatids are correctly attached to the spindle 
microtubules. Because the separation of the sister chromatids during 


anaphase is an irreversible step, the cycle will not proceed until the 
kinetochores of each pair of sister chromatids are firmly anchored to spindle 
fibers arising from opposite poles of the cell. 


Cancer and the Cell Cycle 


Introduction 
" While there are several chronic diseases more destructive to life than 
cancer, none is more feared." Charles Mayo, 1926 


Mayo's words are still true today; a diagnosis of cancer is a fearful thing. 
But what is cancer? Cancer is a collective name for many different 
diseases caused by a common mechanism: uncontrolled cell division. 
Despite the redundancy and overlapping levels of control of cell division, 
errors occur. One of the critical processes monitored by the cell-cycle 
checkpoint surveillance mechanism is the proper replication of DNA during 
the S phase. Even when all of the cell-cycle controls are fully functional, a 
small percentage of replication errors (mutations) will be passed on to the 
daughter cells. If one of these changes to the DNA nucleotide sequence 
occurs within a gene, a gene mutation results. All cancers begin when a 
gene mutation gives rise to a faulty protein that participates in the process 
of cell reproduction. The change in the cell that results from the malformed 
protein may be minor. Even minor mistakes, however, may allow 
subsequent mistakes to occur more readily. Over and over, small, 
uncorrected errors are passed from parent cell to daughter cells and 
accumulate as each generation of cells produces more non-functional 
proteins from uncorrected DNA damage. Eventually, the pace of the cell 
cycle speeds up as the effectiveness of the control and repair mechanisms 
decreases. Uncontrolled growth of the mutated cells outpaces the growth of 
normal cells in the area, and a cancerous tumor can result. 


Some definitions 

All of us have heard the words cancer, tumor, malignancy, metastasis, etc. 
But it is important to understand the definitions of these words, and others, 
before we get into a discussion of the causes of the disease we know as 
cancer. In previous sections you learned about the cell cycle, which controls 
mitosis, and thus controls the growth of cells, tissues, and organs. If there is 
a malfunction at one of the checkpoints of the cell cycle, leading to mitosis 
in cells that would otherwise not divide, it would result in a population of 
cells which have lost control over how and when they divide. This 
accumulation of cells is called a neoplasm (from the Greek veo- neo- "new" 


and mAdopa plasma "formation, creation"). A neoplasm that forms a visible 
or palpable lump in the body is called a tumor. Tumors can be benign, or 
malignant, depending on how fast they grow and how readily (or not) they 
spread to other tissues. An example of a benign tumor would be a wart. 
These usually grow slowly and the cells, although they have lost cell-cycle 
control, do not spread to adjacent or distant tissues. A malignant neoplasm 
is what most people would call cancer; it grows more rapidly and can 
spread to adjacent or even distant sites in the body (a process known as 
metastasis. The number of blood vessels providing nutrients to the tumor 
may also increase (a process known as tumor angiogenesis). 


Characteristics of cancer cells 


What are the characteristics of a cancer cell, and how does it differ from a 
normal cell? Over the decades scientists have discovered many 
morphological and physiological differences ([link]), and studying those 
differences led to many of the advances in our knowledge of the cell cycle 
and its regulation. Cancer biologists have summarized and analyzed many 
of these known differences. It is known that cancer can result from 
mutations in many genes, and that cancers in different organs differ in their 
physiology, appearance, growth rate, and many other parameters. But when 
they filtered through all the data, they concluded that there are six essential 
alterations in cell physiology that are important hallmarks of the malignant 
state. 

Cancer and normal cells 


Normal and Cancer Cells 
under the microscope 


Large, variably shaped nuclei 


Many dividing cells; 


Y 


x P isd 
<= ~~... | Disorganized arrangement 


fone 
ee re 
ae 4 
ie SS 


Variation in size and shape 


Loss of normal features 


Some characteristics of cancer cells, compared to normal cells. Figure 
courtesy of Dr. Wayne LaMorte, Boston University School of Public 
Health. 


e Self-sufficiency in growth signals (positive cell-cycle regulators): 
Cancer cells have an unregulated ability to proliferate. This 
uncontrolled mitosis often occurs via the activation of oncogenes 
(literally, a gene that can cause cancer). Many of these genes code for 
enzymes, such as the protein kinase known as Cdk (see below) or Src, 
which become hyperactive when mutated; this hyperactivity drives 
unregulated cell proliferation (see below). 

e Insensitivity to growth-inhibitory signals (negative cell cycle 
regulators): Cancer cells inactivate so-called tumor suppressor genes, 


such as RB1 or p53 (see below), that normally act at certain points in 
the cell cycle to inhibit mitosis (see below). 

e Evasion of programmed cell death (apoptosis): cancer cells suppress 
and inactivate genes and pathways that normally cause cells to die. 

e Unlimited replication potential: Cancer cells activate specific gene 
pathways that render them immortal even after generations of growth. 
HeLa cells, a human cancer cell derived from a cervical carcinoma in 
the 1950's, are busily proliferating in labs around the world today, long 
after the cancer victim passed away. 

e Sustained angiogenesis (ability to make new blood vessels and obtain 
nutrients via increased blood flow): Many cancer cells acquire the 
capacity to induce growth of blood vessels into the tumor; this is 
known as tumor angiogenesis. 

e Tissue invasion and metastasis: Most normal cells do not migrate, nor 
do they invade surrounding tissues; cancer cells acquire the capacity to 
migrate to other organs, invade other tissues, and colonize these 
organs, resulting in their spread throughout the body. This process is 
called metastasis. 


Proto-oncogenes 


The genes that code for the positive cell-cycle regulators are called proto- 
oncogenes. Proto-oncogenes are normal genes that, when mutated, become 
oncogenes—¢genes that cause a cell to become cancerous. Consider what 
might happen to the cell cycle in a cell with a recently acquired oncogene. 
In most instances, the alteration of the DNA sequence will result in a less 
functional (or non-functional) protein. The result is detrimental to the cell 
and will likely prevent the cell from completing the cell cycle; however, the 
organism is not harmed because the mutation will not be carried forward. If 
a cell cannot reproduce, the mutation is not propagated and the damage is 
minimal. Occasionally, however, a gene mutation causes a change that 
increases the activity of a positive regulator. For example, a mutation that 
allows Cdk, a protein involved in cell-cycle regulation, to be activated 
before it should be could push the cell cycle past a checkpoint before all of 
the required conditions are met. If the resulting daughter cells are too 
damaged to undertake further cell divisions, the mutation would not be 
propagated and no harm comes to the organism. However, if the atypical 


daughter cells are able to divide further, the subsequent generation of cells 
will likely accumulate even more mutations, some possibly in additional 
genes that regulate the cell cycle. 


The Cdk example is only one of many genes that are considered proto- 
oncogenes. In addition to the cell-cycle regulatory proteins, any protein that 
influences the cycle can be altered in such a way as to override cell-cycle 
checkpoints. Once a proto-oncogene has been altered such that there is an 
increase in the rate of the cell cycle, it is then called an oncogene. 


Tumor Suppressor Genes 


Like proto-oncogenes, many of the negative cell-cycle regulatory proteins 
were discovered in cells that had become cancerous. Tumor suppressor 
genes are genes that code for the negative regulator proteins, the type of 
regulator that—when activated—can prevent the cell from undergoing 
uncontrolled division. The collective function of the best-understood tumor 
suppressor gene proteins, retinoblastoma protein (RB1), p53, and p21, is to 
put up a roadblock to cell-cycle progress until certain events are completed. 
A cell that carries a mutated form of a negative regulator might not be able 
to halt the cell cycle if there is a problem. 


Mutated p53 genes have been identified in more than half of all human 
tumor cells. This discovery is not surprising in light of the multiple roles 
that the p53 protein plays at the G, checkpoint. The p53 protein activates 
other genes whose products halt the cell cycle (allowing time for DNA 
repair), activates genes whose products participate in DNA repair, or 
activates genes that initiate cell death when DNA damage cannot be 
repaired. A damaged p53 gene can result in the cell behaving as if there are 
no mutations ([link]). This allows cells to divide, propagating the mutation 
in daughter cells and allowing the accumulation of new mutations. In 
addition, the damaged version of p53 found in cancer cells cannot trigger 
cell death. 


= Cells can become cancerous 


When cellular damage occurs. p53 arrests Mutated p53 does not arrest the cell cycle. 
the cell cycle until the damage is repaired. The damaged cell continues to divide, 

If damage cannot be repaired, apoptosis which may result in cancer. 

occurs. 


(a) The role of p53 is to monitor DNA. If damage is 
detected, p53 triggers repair mechanisms. If repairs are 
unsuccessful, p53 signals apoptosis. (b) A cell with an 
abnormal p53 protein cannot repair damaged DNA and 

cannot signal apoptosis. Cells with abnormal p53 can 
become cancerous. (credit: modification of work by 
Thierry Soussi) 


Transcription 


Introduction 

"My own thinking (and that of many of my colleagues) is based on two 
general principles, which I shall call the Sequence Hypothesis and the 
Central Dogma. The direct evidence for both of them is negligible, but I 
have found them to be of great help in getting to grips with these very 
complex problems. I present them here in the hope that others can make 
similar use of them. Their speculative nature is emphasized by their names. 
It is an instructive exercise to attempt to build a useful theory without using 
them. One generally ends in the wilderness. The Sequence Hypothesis 
This has already been referred to a number of times. In its simplest form it 
assumes that the specificity of a piece of nucleic acid is expressed solely by 
the sequence of its bases, and that this sequence is a (simple) code for the 
amino acid sequence of a particular protein... The Central Dogma This 
states that once ‘information’ has passed into protein it cannot get out again. 
In more detail, the transfer of information from nucleic acid to nucleic acid, 
or from nucleic acid to protein may be possible, but transfer from protein to 
protein, or from protein to nucleic acid is impossible. Information means 
here the precise determination of sequence, either of bases in the nucleic 
acid or of amino acid residues in the protein. This is by no means 
universally held—Sir Macfarlane Burnet, for example, does not subscribe 
to it—but many workers now think along these lines. As far as I know it has 
not been explicitly stated before. " Francis Crick, 1958 


Crick's concept of the Central Dogma of Molecular Biology is a useful way 
to summarize a lot of what we know about nucleic acids. In both 
prokaryotes and eukaryotes, the second function of DNA (the first was 
replication) is to provide the information needed to construct the proteins 
necessary so that the cell can perform all of its functions. To do this, the 
DNA is “read” or transcribed into an mRNA molecule. The mRNA then 
provides the code to form a protein by a process called translation. Through 
the processes of transcription and translation, a protein is built with a 
specific sequence of amino acids that was originally encoded in the DNA. 
This section discusses the details of transcription. 


The Central Dogma of Molecular Biology: DNA Encodes RNA; 
RNA Encodes Protein 


The flow of genetic information in cells from DNA to mRNA to protein is 
described by the Central Dogma of Molecular Biology ((link]), which 
States that genes specify the sequences of mRNAs, which in turn specify the 
sequences of proteins. 


Protein 


The central dogma of molecular 
biology states that DNA encodes 
RNA, which in turn encodes 
protein. 


The copying of DNA to mRNA is relatively straightforward, with one 
nucleotide being added to the mRNA strand for every complementary 
nucleotide read in the DNA strand. The translation to protein is more 
complex because groups of three mRNA nucleotides correspond to one 
amino acid of the protein sequence. However, as we shall see in the next 
section, the translation to protein is still systematic, such that nucleotides 1 
to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino 
acid 2, and so on. 


Transcription: from DNA to mRNA 


Both prokaryotes and eukaryotes perform fundamentally the same process 
of transcription, with the important difference of the membrane-bound 
nucleus in eukaryotes. With the genes bound in the nucleus, transcription 
occurs in the nucleus of the cell and the mRNA transcript must be 
transported to the cytoplasm. The prokaryotes, which include bacteria and 
archaea, lack membrane-bound nuclei and other organelles, and 
transcription occurs in the cytoplasm of the cell. In both prokaryotes and 
eukaryotes, transcription occurs in three main stages: initiation, elongation, 
and termination. 


Initiation 


Transcription requires the DNA double helix to partially unwind in the 
region of mRNA synthesis. The region of unwinding is called a 
transcription bubble. The DNA sequence onto which the proteins and 
enzymes involved in transcription bind to initiate the process is called a 
promoter. In most cases, promoters exist upstream of the genes they 
regulate. The specific sequence of a promoter is very important because it 
determines whether the corresponding gene is transcribed all of the time, 
some of the time, or hardly at all ([link]). 


DNA RNA 
nontemplate 
strand 


RNA polymerase 


DNA 
template 
strand Promoter 


The initiation of transcription begins 
when DNA is unwound, forming a 
transcription bubble. Enzymes and 


other proteins involved in 
transcription bind at the promoter. 


Elongation 


Transcription always proceeds from one of the two DNA strands, which is 
called the template strand. The mRNA product is complementary to the 
template strand and is almost identical to the other DNA strand, called the 
nontemplate strand, with the exception that RNA contains a uracil (U) in 
place of the thymine (T) found in DNA. During elongation, an enzyme 
called RNA polymerase proceeds along the DNA template adding 
nucleotides by base pairing with the DNA template in a manner similar to 
DNA replication, with the difference that an RNA strand is being 
synthesized that does not remain bound to the DNA template. As elongation 
proceeds, the DNA is continuously unwound ahead of the core enzyme and 
rewound behind it ([link]). 


Nontemplate strand 


G 


CcGCACTC 
ATGCCGCA 4 


Dj . “4 
““Ection of Be ea 3 


© 
v GATSSTSCAT 


5 3’ 
TACCACGTA 


CS 
UY 
TASSSSS7 1 CACC Che CAUS 


3 
TGeotcaGtaS 


5! 


DNA RNA polymerase Template strand 


During elongation, RNA polymerase tracks along the 
DNA template, synthesizes mRNA in the 5' to 3' 
direction, and unwinds then rewinds the DNA as it is 
read. 


Termination 


Once a gene is transcribed, the prokaryotic polymerase needs to be 
instructed to dissociate from the DNA template and liberate the newly made 
mRNA. Depending on the gene being transcribed, there are two kinds of 
termination signals, but both involve repeated nucleotide sequences in the 
DNA template that result in RNA polymerase stalling, leaving the DNA 
template, and freeing the mRNA transcript. 


On termination, the process of transcription is complete. In a prokaryotic 
cell, by the time termination occurs, the transcript would already have been 
used to partially synthesize numerous copies of the encoded protein because 
these processes can occur concurrently using multiple ribosomes 
(polyribosomes) ([link]). In contrast, the presence of a nucleus in eukaryotic 
cells precludes simultaneous transcription and translation. 


+ Polyribosome 


Multiple polymerases can transcribe a single 
bacterial gene while numerous ribosomes 
concurrently translate the mRNA transcripts 
into polypeptides. In this way, a specific 
protein can rapidly reach a high 
concentration in the bacterial cell. 


Eukaryotic RNA Processing 


The newly transcribed eukaryotic mRNAs must undergo several processing 
steps before they can be transferred from the nucleus to the cytoplasm and 
translated into a protein. The additional steps involved in eukaryotic MRNA 
maturation create a molecule that is much more stable than a prokaryotic 
mRNA. For example, eukaryotic mRNAs last for several hours, whereas the 
typical prokaryotic mRNA lasts no more than five seconds. 


The mRNA transcript is first coated in RNA-stabilizing proteins to prevent 
it from degrading while it is processed and exported out of the nucleus. This 
occurs while the pre-mRNA still is being synthesized by adding a special 
nucleotide “cap” to the 5' end of the growing transcript. In addition to 
preventing degradation, factors involved in protein synthesis recognize the 
cap to help initiate translation by ribosomes. 


Once elongation is complete, an enzyme then adds a string of 
approximately 200 adenine residues to the 3' end, called the poly-A tail. 
This modification further protects the pre-mRNA from degradation and 
signals to cellular factors that the transcript needs to be exported to the 
cytoplasm. 


Eukaryotic genes are composed of protein-coding sequences called exons 
(ex-on signifies that they are expressed) and intervening sequences called 
introns (int-ron denotes their intervening role). Introns are removed from 
the pre-mRNA during processing. Intron sequences in MRNA do not 
encode functional proteins. It is essential that all of a pre-mRNA’s introns 
be completely and precisely removed before protein synthesis so that the 
exons join together to code for the correct amino acids. If the process errs 
by even a single nucleotide, the sequence of the rejoined exons would be 
shifted, and the resulting protein would be nonfunctional. The process of 
removing introns and reconnecting exons is called splicing ({link]). Introns 
are removed and degraded while the pre-mRNA is still in the nucleus. 


Primary RNA transcript 


l RNA processing 


Spliced RNA 


5' cap Poly-A tail 


5’ untranslated 3’ untranslated 
region region 


Eukaryotic MRNA contains introns that 
must be spliced out. A 5' cap and 3' tail 
are also added. 


Translation 


Introduction 
" Protein synthesis is a central problem for the whole of biology, and that it 
is in all probability closely related to gene action. " Francis Crick, 1958 


Crick's words are still true today. The synthesis of proteins is one of a cell’s 
most complicated and energy-consuming metabolic processes, and the 
evolution of this complex process remains one of the hardest questions to 
answer. But the products of protein synthesis (proteins) indeed are closely 
related to gene action. In addition, proteins account for more mass than any 
other component of living organisms (with the exception of water), and 
proteins perform a wide variety of the functions of a cell. The process of 
translation, or protein synthesis, involves decoding an mRNA message into 
a polypeptide product, in which amino acids are covalently strung together 
in lengths ranging from approximately 50 amino acids to more than 1,000. 


The Protein Synthesis Machinery 


In addition to the mRNA template, many other molecules contribute to the 
process of translation. The composition of each component may vary across 
species; for instance, ribosomes may consist of different numbers of 
ribosomal RNAs (rRNA) and polypeptides depending on the organism. 
However, the general structures and functions of the protein synthesis 
machinery are comparable from bacteria to human cells. Translation 
requires the input of an mRNA template, ribosomes, tRNAs, and various 
enzymatic factors ([link]). 


Amino acids 


Growing 


protein chain Ribosome 


tRNA 


mRNA 


The protein synthesis machinery 
includes the large and small 
subunits of the ribosome, mRNA, 
and tRNA. (credit: modification of 
work by NIGMS, NIH) 


In E. coli, there are 200,000 ribosomes present in every cell at any given 
time. A ribosome is a complex macromolecule composed of structural and 
catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the 
nucleolus is completely specialized for the synthesis and assembly of 
rRNAs. 


Ribosomes are located in the cytoplasm and on the plasma membrane of 
prokaryotes, and in the cytoplasm and endoplasmic reticulum of eukaryotes. 
Ribosomes are made up of a large and a small subunit that come together 
for translation. The small subunit is responsible for binding the mRNA 
template, whereas the large subunit sequentially binds tRNAs, a type of 
RNA molecule that brings amino acids to the growing chain of the 
polypeptide. Each mRNA molecule is simultaneously translated by many 
ribosomes, all synthesizing protein in the same direction. 


Depending on the species, 40 to 60 types of tRNA exist in the cytoplasm. 
Serving as adaptors, specific tRNAs bind to sequences on the mRNA 


template and add the corresponding amino acid to the polypeptide chain. 
Therefore, tRNAs are the molecules that actually “translate” the language 
of RNA into the language of proteins. For each tRNA to function, it must 
have its specific amino acid bonded to it. In the process of tRNA 
“charging,” each tRNA molecule is bonded to its correct amino acid. 


The Genetic Code 


To summarize what we know to this point, the cellular process of 
transcription generates messenger RNA (MRNA), a mobile molecular copy 
of one or more genes with an alphabet of A, C, G, and uracil (U). 
Translation of the mRNA template converts nucleotide-based genetic 
information into a protein product. Protein sequences consist of 20 
commonly occurring amino acids; therefore, it can be said that the protein 
alphabet consists of 20 letters. Each amino acid is defined by a three- 
nucleotide sequence called the triplet codon. The relationship between a 
nucleotide codon and its corresponding amino acid is called the genetic 
code. 


Given the different numbers of “letters” in the mRNA and protein 
“alphabets,” combinations of nucleotides corresponded to single amino 
acids. Using a three-nucleotide code means that there are a total of 64 (4 x 4 
x 4) possible combinations; therefore, a given amino acid is encoded by 
more than one nucleotide triplet ({link]). 


Second letter 


First letter 


Third letter 


This figure shows the genetic code for translating 
each nucleotide triplet, or codon, in MRNA into an 
amino acid or a termination signal in a nascent 
protein. (credit: modification of work by NIH) 


Three of the 64 codons terminate protein synthesis and release the 
polypeptide from the translation machinery. These triplets are called stop 
codons. Another codon, AUG, also has a special function. In addition to 
specifying the amino acid methionine, it also serves as the start codon to 
initiate translation. The reading frame for translation is set by the AUG start 
codon near the 5' end of the mRNA. The genetic code is universal. With a 
few exceptions, virtually all species use the same genetic code for protein 
synthesis, which is powerful evidence that all life on Earth shares a 
common origin. 


The Mechanism of Protein Synthesis 


Just as with mRNA synthesis, protein synthesis can be divided into three 
phases: initiation, elongation, and termination. The process of translation is 
similar in prokaryotes and eukaryotes. Here we will explore how translation 
occurs in E. coli, a representative prokaryote, and specify any differences 
between prokaryotic and eukaryotic translation. 


Protein synthesis begins with the formation of an initiation complex. In E. 
coli, this complex involves the small ribosome subunit, the mRNA 
template, three initiation factors, and a special initiator tRNA. The initiator 
tRNA interacts with the AUG start codon, and links to a special form of the 
amino acid methionine that is typically removed from the polypeptide after 
translation is complete. 


In prokaryotes and eukaryotes, the basics of polypeptide elongation are the 
same, so we will review elongation from the perspective of E. coli. The 
large ribosomal subunit of E. coli consists of three compartments: the A site 
binds incoming charged tRNAs (tRNAs with their attached specific amino 
acids). The P site binds charged tRNAs carrying amino acids that have 
formed bonds with the growing polypeptide chain but have not yet 
dissociated from their corresponding tRNA. The E site releases dissociated 
tRNAs so they can be recharged with free amino acids. The ribosome shifts 
one codon at a time, catalyzing each process that occurs in the three sites. 
With each step, a charged tRNA enters the complex, the polypeptide 
becomes one amino acid longer, and an uncharged tRNA departs. The 
energy for each bond between amino acids is derived from GTP, a molecule 
similar to ATP ([link]). Amazingly, the E. coli translation apparatus takes 
only 0.05 seconds to add each amino acid, meaning that a 200-amino acid 
polypeptide could be translated in just 10 seconds. 


Ribosome large 
subunit 


Small Ribosomal 
subunit 


Polypeptide chain 


Translation begins when a tRNA 
anticodon recognizes a codon on 
the mRNA. The large ribosomal 
subunit joins the small subunit, 
and a second tRNA is recruited. 
As the mRNA moves relative to 
the ribosome, the polypeptide 
chain is formed. Entry of a release 
factor into the A site terminates 
translation and the components 
dissociate. 


Termination of translation occurs when a stop codon (UAA, UAG, or UGA) 
is encountered. When the ribosome encounters the stop codon, the growing 
polypeptide is released and the ribosome subunits dissociate and leave the 
mRNA. After many ribosomes have completed translation, the mRNA is 
degraded so the nucleotides can be reused in another transcription reaction. 


Connection Between DNA and Phenotype 
You CAN get there from here... 


In the beginning was the word 
WORD 

WORE 

GORE 

GONE 

GENE 

and by the mutation came the gene. 


Michael A. Arbib, Towards a Theoretical Biology: An IUBS Symposium, 
1969 


Sickle Cell Anemia: A look at the connection between DNA and 
Phenotype 


Changes in the DNA sequence of a gene are known as mutations. Because 
genes code for and are translated into proteins, mutations often (but not 
always) result in changes in the sequence of amino acids in those proteins. 
Changes in the amino acid sequence can modify or even completely destroy 
protein function. Proteins have many functions within cells, and a change in 
those functions results in a change in the phenotype of that cell or organism. 
So a mutation as simple as a single base change in a DNA sequence can 
have dramatic effects on phenotype. One of the best examples of this 
phenomenon can be observed when mutations occur in the gene for one of 
the protein components of the red blood cell protein we call hemoglobin. 


A major component of the erythrocytes (red blood cells) found in ver- 
tebrates is hemoglobin. A molecule of hemoglobin from a normal adult 
human contains 4 proteins (two identical alpha polypeptides and two 
identical beta polypeptides) surrounding a core of heme (contains complex 
molecule containing an atom of iron which can combine reversibly with 
oxygen). Thus, hemoglobin functions as the major oxygen-carrying 
constituent of blood. Because of hemoglobin, a given volume of blood can 
carry far more oxygen than could be dissolved in an equal volume of water. 


The polypeptides that make up the hemoglobin are produced by the 
processes of transcription and translation. So, the instructions for making 
the polypeptides are stored in the DNA, and the specific region on the DNA 
that codes for the polypeptide is called a gene. The physical location of the 
gene on the chromosome is the locus. If you remember from the earlier 
section on protein structure and function, the sequence of amino acids in a 
polypeptide can have a significant effect on the overall function of the 
protein. Since the sequence of nucleotides in the DNA codes for a particular 
sequence of amino acids in the polypeptide, it is logical to conclude that 
changes in the nucleotide sequence in the DNA can change the sequence of 
amino acids in the polypeptide and thereby changing how the polypeptide 
functions. 


In many human populations, particularly those with origins in Central 
Africa or the Mediterranean, there are individuals who suffer from severe 
anemia and whose blood contains numerous distorted, sickle-shaped 
erythrocytes ([link]). Hence, the disease was given the name sickle-cell 
anemia. 


Notice the sickle shaped cells in the image. By 
Dr Graham Beards via Wikimedia Commons 


Sickle-cell anemia is one of the most studied and well-understood genetic 
diseases. In spite of this level of understanding, there is currently no 
effective treatment for the disease. Experimental bone marrow transplants 
have cured the disease in some patients, but bone marrow transplants are 
currently recommended in only a handful of cases. In the United States 
alone, there are 50,000 individuals with sickle-cell anemia. 


Biochemical studies established that the gene affected in sickle-cell anemia 
has the code for an abnormal beta polypeptide, which is one of the 
components of the hemoglobin molecule. Therefore, there are two different 
forms of the hemoglobin gene that codes for the beta chain: 


Form 1: Hb“ has the code for a normal beta chain 
Form 2: Hb has the code for an abnormal beta chain 


Hb“ and HbS are considered alleles. The word “allele” comes from the 
same root as “alternative.” Thus, alleles are alternative forms of the same 
gene. Alleles arise by mutation. Mutations come about by many different 
ways, but what is common among the different types of mutations is a 
change in the order of nucleotides in the DNA. Thinking back to the Central 
Dogma of Molecular Biology, one can reword it with the above in mind. 
Changes in the DNA causes changes in RNA which can cause changes in 
the polypeptide and a new polypeptide is a new phenotype. 


Humans are diploid organisms; they have two copies of most genes. 
However, the two copies they possess do not have to be identical. When 
there are two possible alleles for a gene (such as in the gene for the beta 
chain of hemoglobin), a diploid individual will have one of three possible 
combinations of the two alleles. They can be Hb“ Hb“ , Hb“ Hb, or Hb*® 
Hb*. 


The set of alleles present in an individual for a given gene is known as the 
individual’s genotype. The three combinations of two alleles above are 
therefore the three different genotypes. Individuals that have two copies of 
the same allele are called homozygous; individuals with two different 


alleles are called heterozygous. So, an individual that is Hb“ Hb“ is 
homozygous normal beta chain, an individual that is Hb“ Hb is 
heterozygous, and an individual that is Hb* Hb® is homozygous abnormal 
beta chain. 


There is one more term that you need to know: the expression of the 
particular combination of alleles an individual has at a locus is known as the 
individual’s phenotype. The phenotype is really nothing more than the final 
end product of the genes and their interaction with the environment. 


Homozygous Hb® Hb® individuals (called sickle-cell anemics) can have 
many sickle-shaped (as opposed to normal disc-shaped) erythrocytes in 
their blood. How does this occur? The process is well-understood, and 
summarized below. 


In the capillaries (microscopic blood vessels that directly exchange oxygen 
with the tissues), erythrocytes can be subjected to low oxygen tension after 
they lose their oxygen to the surrounding tissues. In this low oxygen 
situation, the abnormal hemoglobin molecules of Hb* Hb® individuals tend 
to polymerize (join together), forming stiff, tubular fibers which ultimately 
distort the shape of the entire erythrocyte, giving it the characteristic 
“sickle” shape. These sickled cells have a number of effects on the body via 
two processes. 


1. The sickle-shape affects capillary blood flow: 

Sickled cells are less able to enter and move through the capillaries. 
Once in the capillaries, they clog capillary flow and cause small blood 
clots. 

Reduced blood flow results in reduced oxygen availability to the 
tissues. 

Reduced oxygen supply results in tissue death and damage to vital 
organs (e.g., the heart, liver and spleen). 

2. Sickled blood cells have a shorter lifespan than normal red blood 
cells: 

Reduced lifespan of erythrocytes places a greater demand on the bone 
marrow to make new red blood cells and on the spleen to break down 
dead erythrocytes. 


Increased demand on the bone matrow results in severe pain in the 
long bones and joints. 

Individuals suffering from sickle-cell anemia are frequently ill and 
generally have a considerably reduced lifespan. These individuals 
are said to have sickle-cell disease. 


Homozygous Hb“ Hb4 individuals have erythrocytes which retain their 
normal shape in the body and which retain normal shape even when blood 
samples are subjected to greatly reduced oxygen tension in laboratory tests. 


Heterozygous individuals (Hb“ Hb‘) are said to be carriers for sickle-cell 
anemia. Note: this is a specific term and is not the same thing as sickle cell 
anemia—heterozygotes do not have the disease themselves but their 
children may inherit the condition. Carriers have no anemia, do have good 
health (as do Hb“ Hb4 individuals) and their erythrocytes maintain normal 
shape in the blood. In other words, they are phenotypically normal under 
most conditions, and probably do not know that they “carry” the Hb® allele. 
However, if heterozygotes are exposed to conditions of low oxygen levels 
(such as strenuous activity at high altitudes) some of their erythrocytes do 
sickle. Red blood cells in blood samples of heterozygotes subjected to 
greatly reduced oxygen tension in the laboratory also sickle. 


Why is sickle cell anemia most prevalent in people with origins in Central 
Africa and the Mediterranean? If you look at the figure below ({link]) , you 
will see the occurrence of sickle cell anemia overlaps with the 
pervasiveness of malaria. This seems odd, but those individuals how are 
heterozygous (Hb“ Hb‘) for the sickle cell allele are less likely to contract 
and die from malaria then those who are homozygous (Hb“ Hb“). The Hb 
polypeptide that is produced by the heterozygous individual stops the 
organism (Plasmodium) that causes malaria from invading the red blood 
cells. So, in areas where malaria is common there is selection pressure for 
the Hb® allele, and the Hb® allele occurs in a higher frequency because the 
those who have one copy of the Hb® allele will live longer and have more 
children. In areas where malaria is not common, there is selection pressure 
against the Hb® allele, and the Hb® allele occurs in a lower frequency. As 
you will learn in a later chapter, there is an 25% chance that two carriers 
will have a child who is homozygous Hb® Hb‘), and this child will pay the 


evolutionary price for the protection from malaria that the parents were 
afforded. Hopefully, you will now understand how evolution favors the 
presence of such a potentially detrimental allele in a population. The sickle 
cell example is only one of what is called heterozygous advantage, we have 
provided a number of other examples in [link]. 


The hatched line represents the distribution of malaria. The various red 
colors represent the relative frequency of sickle cell allele in the 
population with the dark red having the highest frequency and the light 
red having the lowest frequency. Work by Eva Horne. 


Recessive 
Illness 


Cystic fibrosis 


G6PD 
Deficiency 


Phenylketonuria 
(PKU) 


Tay-Sachs 
disease 


Noninsulin- 
dependent 
diabetes 
mellitus 


Heterozygote 
Advantage 


protection 
against diarrheal 
diseases such as 
cholera 


Protection 
against malaria 


Protection 
against 
miscarriage 
induced by a 
fungal toxin 


Protection 
against 
tuberculosis 


Protection 
against 
starvation 


Possible Explanation 


Carriers have too few 
functional chloride 
channels in intestinal 
cells, blocking toxin 


Red blood cells 
inhospitable to malaria 


Excess amino acid 
(phenylalanine) in carriers 
inactivates toxin 


Unknown 


Tendency to gain weight 
protects against starvation 
during famine 


Examples of Heterozygous Advantage in Humans 


Sexual Reproduction 


Introduction 

"Being the inventor of sex would seem to be a sufficient distinction for a 
creature just barely large enough to be seen by the naked eye. [Comment 
about Volvox, a freshwater green algae, which appears indetermimately 
plantlike and animal-like during its reproductive cycle.] " Joseph Wood 
Krutch, 1957 


Sexual reproduction was an early evolutionary innovation after the 
appearance of eukaryotic cells. The fact that most eukaryotes reproduce 
sexually is evidence of its evolutionary success. In many animals, it is the 
only mode of reproduction. And yet, scientists recognize some real 
disadvantages to sexual reproduction. On the surface, offspring that are 
genetically identical to the parent may appear to be more advantageous. If 
the parent organism is successfully occupying a habitat, offspring with the 
same traits would be similarly successful. There is also the obvious benefit 
to an organism that can produce offspring by asexual budding, 
fragmentation, or asexual eggs. These methods of reproduction do not 
require another organism of the opposite sex. There is no need to expend 
energy finding or attracting a mate. That energy can be spent on producing 
more offspring. Indeed, some organisms that lead a solitary lifestyle have 
retained the ability to reproduce asexually. In addition, asexual populations 
only have female individuals, so every individual is capable of 
reproduction. In contrast, the males in sexual populations (half the 
population) are not producing offspring themselves. Because of this, an 
asexual population can grow twice as fast as a sexual population in theory. 
This means that in competition, the asexual population would have the 
advantage. All of these advantages to asexual reproduction, which are also 
disadvantages to sexual reproduction, should mean that the number of 
species with asexual reproduction should be more common. 


However, multicellular organisms that exclusively depend on asexual 
reproduction are exceedingly rare. Why is sexual reproduction so common? 
This is one of the important questions in biology and has been the focus of 
much research from the latter half of the twentieth century until now. A 
likely explanation is that the variation that sexual reproduction creates 


among offspring is very important to the survival and reproduction of those 
offspring. The only source of variation in asexual organisms is mutation. 
This is the ultimate source of variation in sexual organisms. In addition, 
those different mutations are continually reshuffled from one generation to 
the next when different parents combine their unique genomes, and the 
genes are mixed into different combinations by the process of meiosis. 
Meiosis is the division of the contents of the nucleus that divides the 
chromosomes among gametes. Variation is introduced during meiosis, as 
well as when the gametes combine in fertilization. 


Note: 

Evolution in Action 

The Red Queen Hypothesis 

There is no question that sexual reproduction provides evolutionary 
advantages to organisms that employ this mechanism to produce offspring. 
The problematic question is why, even in the face of fairly stable 
conditions, sexual reproduction persists when it is more difficult and 
produces fewer offspring for individual organisms? Variation is the 
outcome of sexual reproduction, but why are ongoing variations necessary? 
Enter the Red Queen hypothesis, first proposed by Leigh Van Valen in 
1973, {footnote The concept was named in reference to the Red Queen's race 
in Lewis Carroll's book, Through the Looking-Glass, in which the Red 
Queen says one must run at full speed just to stay where one is. 

Leigh Van Valen, “A new evolutionary law,” Evolutionary Theory 1 
(1973): 1-30. 

All species coevolve with other organisms. For example, predators 
coevolve with their prey, and parasites coevolve with their hosts. A 
remarkable example of coevolution between predators and their prey is the 
unique coadaptation of night flying bats and their moth prey. Bats find their 
prey by emitting high-pitched clicks, but moths have evolved simple ears 
to hear these clicks so they can avoid the bats. The moths have also 
adapted behaviors, such as flying away from the bat when they first hear it, 
or dropping suddenly to the ground when the bat is upon them. Bats have 
evolved “quiet” clicks in an attempt to evade the moth’s hearing. Some 


moths have evolved the ability to respond to the bats’ clicks with their own 
clicks as a strategy to confuse the bats echolocation abilities. 

Each tiny advantage gained by favorable variation gives a species an edge 
over close competitors, predators, parasites, or even prey. The only method 
that will allow a coevolving species to keep its own share of the resources 
is also to continually improve its ability to survive and produce offspring. 
AS one species gains an advantage, other species must also develop an 
advantage or they will be outcompeted. No single species progresses too 
far ahead because genetic variation among progeny of sexual reproduction 
provides all species with a mechanism to produce adapted individuals. 
Species whose individuals cannot keep up become extinct. The Red 
Queen’s catchphrase was, “It takes all the running you can do to stay in the 
same place.” This is an apt description of coevolution between competing 
species. 


Life Cycles of Sexually Reproducing Organisms 


Fertilization and meiosis alternate in sexual life cycles. What happens 
between these two events depends on the organism. The process of meiosis 
reduces the resulting gamete’s chromosome number by half. Fertilization, 
the joining of two haploid gametes, restores the diploid condition. The 
number of sets of chromosomes in a cell is called its ploidy level. Haploid 
(1n) cells contain one set of chromosomes. Cells containing two sets of 
chromosomes are called diploid (2n). There are three main categories of life 
cycles in multicellular organisms: diploid-dominant, in which the 
multicellular diploid stage is the most obvious life stage (and there is no 
multicellular haploid stage), as with most animals including humans; 
haploid-dominant, in which the multicellular haploid stage is the most 
obvious life stage (and there is no multicellular diploid stage), as with all 
fungi and some algae; and alternation of generations, in which the two 
stages, haploid and diploid, are apparent to one degree or another depending 
on the group, as with plants and some algae. 


Nearly all animals employ a diploid-dominant life-cycle strategy in which 
the only haploid cells produced by the organism are the gametes. The 


gametes are produced from diploid germ cells, a special cell line that only 
produces gametes. Once the haploid gametes are formed, they lose the 
ability to divide again. There is no multicellular haploid life stage. 
Fertilization occurs with the fusion of two gametes, usually from different 
individuals, restoring the diploid state ({link]a). 


Note: 


Zygospore 


ities 


ASEXUAL 


(a) In animals, sexually reproducing 
adults form haploid gametes from 
diploid germ cells. (b) Fungi, such as 
black bread mold (Rhizopus 


nigricans), have haploid-dominant life 

cycles. (c) Plants have a life cycle that 
alternates between a multicellular 

haploid organism and a multicellular 

diploid organism. (credit c “fern”: 

modification of work by Cory Zanker; 

credit c “gametophyte”: modification 
of work by “VImastra”/Wikimedia 

Commons) 


Most fungi and algae employ a life-cycle strategy in which the multicellular 
“body” of the organism is haploid. During sexual reproduction, specialized 
haploid cells from two individuals join to form a diploid zygote. The zygote 
immediately undergoes meiosis to form four haploid cells called spores 
([link]b). 


The third life-cycle type, employed by some algae and all plants, is called 
alternation of generations. These species have both haploid and diploid 
multicellular organisms as part of their life cycle. The haploid multicellular 
plants are called gametophytes because they produce gametes. Meiosis is 
not involved in the production of gametes in this case, as the organism that 
produces gametes is already haploid. Fertilization between the gametes 
forms a diploid zygote. The zygote will undergo many rounds of mitosis 
and give rise to a diploid multicellular plant called a sporophyte. 
Specialized cells of the sporophyte will undergo meiosis and produce 
haploid spores. The spores will develop into the gametophytes ({link]c). 


Meiosis 


Introduction 

"T may finally call attention to the probability that the association of the 
paternal and maternal chromosomes in pairs, and their subsequent 
separation during the reducing division as indicated above, may constitute 
the physical basis of the Mendelian law of heredity." Walter S. Sutton, "On 
the Morphology of the Chromosome Group in Brachystola 
magna",Biological Bulletin, 1902, 4:39 


Sutton was one of the biologists (along with Theodor Boveri) who 
discovered that chromosomes correspond to the paired "particles" required 
by Mendel's Laws, and that the number of these chromosomes is halved at 
the time that sperm and egg cells are generated. The Boveri-Sutton 
Chromosome Theory (also known as the Chromosome Theory of 
Inheritance) is one of the important linkages between Mendel and modern 
molecular biology. Sutton was raised on a farm near Russell, Kansas, and 
played basketball under Coach Naismith at the University of Kansas. His 
ground-breaking work was done at Columbia University in New York City. 
So when you study meiosis and heredity, remember that a major part of this 
knowledge came from the work of another biologist from Kansas, Walter 
Sutton, working with grasshoppers (the aforementioned Brachystola 
magna) that are indigenous to the state of Kansas. 


Haploid (1n) 


Gametes Diploid (2n) 


Somatic cell 


ie 


Fertilization 


a 


Homologous Pair 
of chromosomes 


The process of fertilization produces a dipliod cell by the union of two 
haploid cells. The homologous pairs are based on size and the color 
refers to the maternal and paternal chromosomes. Work by Robbie 
Bear. 


Sexual reproduction requires fertilization, a union of two cells from two 
individual organisms. If those two cells each contain one set of 
chromosomes, then the resulting cell contains two sets of chromosomes. 
The number of sets of chromosomes in a cell is called its ploidy level. 
Haploid (1n) cells contain one set of chromosomes. Cells containing two 
sets of chromosomes are called diploid (2n) ({link]). If the reproductive 
cycle is to continue, the diploid cell must somehow reduce its number of 
chromosome sets before fertilization can occur again, or there will be a 
continual doubling in the number of chromosome sets in every generation. 


So, in addition to fertilization, sexual reproduction includes a nuclear 
division, known as meiosis, that reduces the number of chromosome sets. 


Most animals and plants are diploid, containing two sets of chromosomes; 
in each somatic cell (the nonreproductive cells of a multicellular organism), 
the nucleus contains two copies of each chromosome that are referred to as 
homologous chromosomes ({link]). Somatic cells are sometimes referred 
to as “body” cells. Homologous chromosomes are matched pairs containing 
genes for the same traits in identical locations along their length. Diploid 
organisms inherit one copy of each homologous chromosome from each 
parent; all together, they are considered a full set of chromosomes. In 
animals, haploid cells containing a single copy of each homologous 
chromosome are found only within gametes. Gametes fuse with another 
haploid gamete to produce a diploid cell. 


Diploid (2n) Diploid (2n) 
Germ cell Germ cell 


DNA Replication and 
Chromosome Duplication 


7» 


Homologous pair 


of chromosomes Homologous pair of 


duplicated chromosomes 
each consisting of sister 
chromatids 


The process of DNA replication produces a duplicated chromosome 
with two sister chromatids in each of the homologous pairs. The 


homologous pairs are based on size and the color refers to the maternal 
and paternal chromosomes. Work by Robbie Bear. 


The nuclear division that forms haploid cells, which is called meiosis, is 
related to mitosis. As you have learned, mitosis is part of a cell reproduction 
cycle that results in identical daughter nuclei that are also genetically 
identical to the original parent nucleus. In mitosis, both the parent and the 
daughter nuclei contain the same number of chromosome sets—diploid for 
most plants and animals. Meiosis employs many of the same mechanisms 
as mitosis. However, the starting nucleus is always diploid and the nuclei 
that result at the end of a meiotic cell division are haploid. To achieve the 
reduction in chromosome number, meiosis consists of one round of 
chromosome duplication ([link]) and two rounds of nuclear division. 
Because the events that occur during each of the division stages are 
analogous to the events of mitosis, the same stage names are assigned. 
However, because there are two rounds of division, the stages are 
designated with a “I” or “II.” Thus, meiosis I is the first round of meiotic 
division and consists of prophase I, metaphase I, and so on. Meiosis I 
reduces the number of chromosome sets from two to one. The genetic 
information is also mixed during this division to create unique recombinant 
chromosomes. Meiosis II, in which the second round of meiotic division 
takes place in a way that is similar to mitosis, includes prophase II, 
pmetaphase IJ, and so on ((link]). 


yng 
G1 


centrioles 
nucleus 
DNA replication = 


Un-replicated, Replicated, 
uncondensed uncondensed 
DNA 


Meiosis |: Products 
2 haploid cells 


Meiosis Il: Prophase 2 


) 


Meiosis Il: Metaphase 2 Meiosis Il: Anaphase 2 


Meiosis |: Prophase 1 Meiosis |: Metaphase 1 


spindle fibers 


£6 


Homologous pair of 
condensed, replicated 
chromosomes in synapsis 


Meiosis |: Telophase 1 


‘G ‘ 


Meiosis II: Telophase 2 


Meiosis |: Anaphase 1 


Meiosis II: Products 


4 haploid cells = gametes 


ee Of 


This image illustrates meiosis for a cell with 2 pairs of homologous 
chromosomes. The homologous pairs are based on size and the color 
refers to the maternal and paternal chromosomes. Work by Eva Horne. 


Interphase 


Meiosis is preceded by an interphase consisting of the Gj, S, and Gp phases, 
which are nearly identical to the phases preceding mitosis. The G, phase is 
the first phase of interphase and is focused on cell growth. In the S phase, 
the DNA of the chromosomes is replicated. Finally, in the G» phase, the cell 
undergoes the final preparations for meiosis. 


During DNA duplication of the S phase, each chromosome becomes 
composed of two identical copies (called sister chromatids) that are held 
together at the centromere until they are pulled apart during meiosis II. In 
an animal cell, the centrosomes that organize the microtubules of the 
meiotic spindle also replicate. This prepares the cell for the first meiotic 
phase. 


Meiosis I 


In prophase I, the chromosomes can be seen clearly microscopically. As the 
nuclear envelope begins to break down, the proteins associated with 
homologous chromosomes bring the pair close to each other. The tight 
pairing of the homologous chromosomes is called synapsis. In synapsis, the 
genes on the chromatids of the homologous chromosomes are precisely 
aligned with each other. An exchange of chromosome segments between 
non-sister homologous chromatids occurs and is called crossing over. 


The crossover events are the first source of genetic variation produced by 
meiosis. A single crossover event between homologous non-sister 
chromatids leads to a reciprocal exchange of equivalent DNA between a 
maternal chromosome and a paternal chromosome. Now, when that sister 
chromatid is moved into a gamete, it will carry some DNA from one parent 
of the individual and some DNA from the other parent. The recombinant 
sister chromatid has a combination of maternal and paternal genes that did 
not exist before the crossover. In the next class period, we will explore how 
crossing over and recombinant sister chromatids influence patterns of 
inheritance. 


The key event in metaphase I is the attachment of the spindle fiber 
microtubules to the kinetochore proteins at the centromeres. The 
microtubules assembled from centrosomes at opposite poles of the cell 


grow toward the middle of the cell. The homologous chromosomes are held 
together and form a tetrad. At the end of metaphase I, each tetrad is 
attached to microtubules from both poles, with one homologous 
chromosome attached at one pole and the other homologous chromosome 
attached to the other pole. In addition, the nuclear membrane has broken 
down entirely. 


By the end metaphase I, the homologous chromosomes are arranged in the 
center of the cell with the kinetochores facing opposite poles. The 
orientation of each pair of homologous chromosomes at the center of the 
cell is random. 


This randomness, called independent assortment, is the physical basis for 
the generation of the second form of genetic variation in offspring. Consider 
that the homologous chromosomes of a sexually reproducing organism are 
originally inherited as two separate sets, one from each parent. Using 
humans as an example, one set of 23 chromosomes is present in the egg 
donated by the mother. The father provides the other set of 23 chromosomes 
in the sperm that fertilizes the egg. In metaphase I, these pairs line up at the 
midway point between the two poles of the cell. Because there is an equal 
chance that a microtubule fiber will encounter a maternally or paternally 
inherited chromosome, the arrangement of the tetrads at the metaphase plate 
is random. Any maternally inherited chromosome may face either pole. 
Any paternally inherited chromosome may also face either pole. The 
orientation of each tetrad is independent of the orientation of the other 22 
tetrads. 


In each cell that undergoes meiosis, the arrangement of the tetrads is 
different. The number of variations depends on the number of chromosomes 
making up a set. There are two possibilities for orientation (for each tetrad); 
thus, the possible number of alignments equals 2” where n is the number of 
chromosomes per set. Humans have 23 chromosome pairs, which results in 
over eight million (27) possibilities. This number does not include the 
variability previously created in the sister chromatids by crossover. Given 
these two mechanisms, it is highly unlikely that any two haploid cells 
resulting from meiosis will have the same genetic composition ((Link]). 


To summarize the genetic consequences of meiosis I: the maternal and 
paternal genes are recombined by crossover events occurring on each 
homologous pair during prophase I; in addition, the random assortment of 
tetrads at metaphase produces a unique combination of maternal and 
paternal chromosomes that will make their way into the gametes. 


Possible Chromosome Arrangement | Possible Chromosome Arrangement II 


Meiosis |: Homologous 
chromosomes separate 


Meiosis |: Homologous 
chromosomes separate 


Meiosis II: Sister 
chromatids separate 


Meiosis Il: Sister 
chromatids separate 


This illustration shows that, in a cell with 2 pairs of 
homologous chromosomes, 2 possible arrangements of 
chromosomes in Meiosis I will give rise to 4 different 
kinds of gametes. These are shown at the bottom of the 
figure; although there are 8 total gametes, there are 4 
pairs that are identical. 


In anaphase I, the spindle fibers pull the homologous chromosomes apart. 
The sister chromatids remain tightly bound together at the centromere 
({link]). 


In telophase I, the separated chromosomes arrive at opposite poles. The 
remainder of the typical telophase events may or may not occur depending 
on the species. In some organisms, the chromosomes decondense and 
nuclear envelopes form around the chromatids in telophase I. 


Cytokinesis, the physical separation of the cytoplasmic components into 
two daughter cells, occurs without reformation of the nuclei in other 
organisms. In nearly all species, cytokinesis separates the cell contents by 
either a cleavage furrow (in animals and some fungi), or a cell plate that 
will ultimately lead to formation of cell walls that separate the two daughter 
cells (in plants). At each pole, there is just one member of each pair of the 
homologous chromosomes, so only one full set of the chromosomes is 
present. This is why the cells are considered haploid—there is only one 
chromosome set, even though there are duplicate copies of the set because 
each homolog still consists of two sister chromatids that are still attached to 
each other. However, although the sister chromatids were once duplicates of 
the same chromosome, they are no longer identical at this stage because of 
crossovers. 


Meiosis II 


In meiosis II, the connected sister chromatids remaining in the haploid cells 
from meiosis I will be split to form four haploid cells ([link]). In some 
species, cells enter a brief interphase, or interkinesis, that lacks an S phase, 


before entering meiosis II. Chromosomes are not duplicated during 
interkinesis. The two cells produced in meiosis I go through the events of 
meiosis II in synchrony. Overall, meiosis II resembles the mitotic division 
of a haploid cell. 


In prophase II, if the chromosomes decondensed in telophase I, they 
condense again. If nuclear envelopes were formed, they fragment into 
vesicles. The centrosomes duplicated during interkinesis move away from 
each other toward opposite poles, and new spindles are formed. In early 
metaphase IT, the nuclear envelopes are completely broken down, and the 
spindle is fully formed. Each sister chromatid forms an individual 
kinetochore that attaches to microtubules from opposite poles. In metaphase 
II, the sister chromatids are maximally condensed and aligned at the center 
of the cell. In anaphase II, the sister chromatids are pulled apart by the 
spindle fibers and move toward opposite poles. 


In telophase II, the chromosomes arrive at opposite poles and begin to 
decondense. Nuclear envelopes form around the chromosomes. Cytokinesis 
separates the two cells into four genetically unique haploid cells. At this 
point, the nuclei in the newly produced cells are both haploid and have only 
one copy of the single set of chromosomes. The cells produced are 
genetically unique because of the random assortment of paternal and 
maternal homologs and because of the recombination of maternal and 
paternal segments of chromosomes—with their sets of genes—that occurs 
during crossover. 


Mendel’s Experiments 


Introduction 

""Mendel's forty-odd year stint at the Brno abbey was, indeed, deeply 
constrained by rules, habits, and limits. He began his experiments on 
inheritance by breeding field mice but was asked to discontinue them 
because forcing mice to mate was considered too risqué for a monk."" S. 
Mukherjee, "On Tenderness", introduction to The Best American Science 
and Nature Writing, Mariner Press, Boston and New York, 2013 


Johann Gregor Mendel 
set the framework for 
the study of genetics. 


Johann Gregor Mendel (1822-1884) ([link]) was a lifelong learner, teacher, 
scientist, and man of faith. As a young adult, he joined the Augustinian 
Abbey of St. Thomas in Bmo in what is now the Czech Republic. 
Supported by the monastery, he taught physics, botany, and natural science 
courses at the secondary and university levels. In 1856, he began a decade- 
long research pursuit involving inheritance patterns in honeybees and 
plants, ultimately settling on pea plants as his primary model system (a 
system with convenient characteristics that is used to study a specific 
biological phenomenon to gain understanding to be applied to other 


systems). In 1865, Mendel presented the results of his experiments with 
nearly 30,000 pea plants to the local natural history society. He 
demonstrated that traits are transmitted faithfully from parents to offspring 
in specific patterns. In 1866, he published his work, Experiments in Plant 
Hybridization, 2"! in the proceedings of the Natural History Society of 
Brunn. 

Johann Gregor Mendel, “Versuche iiber Pflanzenhybriden.” Verhandlungen 
des naturforschenden Vereines in Brtinn, Bd. IV fiir das Jahr, 1865 
Abhandlungen (1866):3—47. [for English translation, see 
http://www.mendelweb.org/Mendel.plain.html] 


Mendel’s work went virtually unnoticed by the scientific community, which 
incorrectly believed that the process of inheritance involved a blending of 
parental traits that produced an intermediate physical appearance in 
offspring. This hypothetical process appeared to be correct because of what 
we know now as continuous variation. Continuous variation is the range of 
small differences we see among individuals in a characteristic like human 
height. It does appear that offspring are a “blend” of their parents’ traits 
when we look at characteristics that exhibit continuous variation. Mendel 
worked instead with traits that show discontinuous variation. Discontinuous 
variation is the variation seen among individuals when each individual 
shows one of two—or a very few—easily distinguishable traits, such as 
violet or white flowers. Mendel’s choice of these kinds of traits allowed him 
to see experimentally that the traits were not blended in the offspring as 
would have been expected at the time, but that they were inherited as 
distinct traits. In 1868, Mendel became abbot of the monastery and 
exchanged his scientific pursuits for his pastoral duties. He was not 
recognized for his extraordinary scientific contributions during his lifetime; 
in fact, it was not until 1900 that his work was rediscovered, reproduced, 
and revitalized by scientists on the brink of discovering the chromosomal 
basis of heredity. 


Mendel’s Crosses 


Mendel’s seminal work was accomplished using the garden pea, Pisum 
sativum, to study inheritance. This species naturally self-fertilizes, meaning 
that pollen encounters ova within the same flower. The flower petals remain 


sealed tightly until pollination is completed to prevent the pollination of 
other plants. The result is highly inbred, or “true-breeding,” pea plants. 
These are plants that always produce offspring that look like the parent. By 
experimenting with true-breeding pea plants, Mendel avoided the 
appearance of unexpected traits in offspring that might occur if the plants 
were not true breeding. The garden pea also grows to maturity within one 
season, meaning that several generations could be evaluated over a 
relatively short time. Finally, large quantities of garden peas could be 
cultivated simultaneously, allowing Mendel to conclude that his results did 
not come about simply by chance. 


Mendel performed hybridizations, which involve mating two true-breeding 
individuals that have different traits. In the pea, which is naturally self- 
pollinating, this is done by manually transferring pollen from the anther of a 
mature pea plant of one variety to the stigma of a separate mature pea plant 
of the second variety. 


Plants used in first-generation crosses were called P, or parental generation, 
plants ([link]). Mendel collected the seeds produced by the P plants that 
resulted from each cross and grew them the following season. These 
offspring were called the Fj, or the first filial (filial = daughter or son), 
generation. Once Mendel examined the characteristics in the F; generation 
of plants, he allowed them to self-fertilize naturally. He then collected and 
grew the seeds from the F, plants to produce the Fy, or second filial, 
generation. Mendel’s experiments extended beyond the F> generation to the 
F3 generation, F, generation, and so on, but it was the ratio of 
characteristics in the P, F;, and F> generations that were the most intriguing 
and became the basis of Mendel’s postulates. 


Hybridization of true-breeding plants 


Self-fertilization of hybrid plants 


Mendel’s process for performing 
crosses included examining flower 
color. 


Garden Pea Characteristics Revealed the Basics of Heredity 


In his 1865 publication, Mendel reported the results of his crosses involving 
seven different characteristics, each with two contrasting traits. A trait is 
defined as a variation in the physical appearance of a heritable 
characteristic. The characteristics included plant height, seed texture, seed 
color, flower color, pea-pod size, pea-pod color, and flower position. For 
the characteristic of flower color, for example, the two contrasting traits 
were white versus violet. To fully examine each characteristic, Mendel 
generated large numbers of F, and F> plants and reported results from 
thousands of F> plants. 


What results did Mendel find in his crosses for flower color? First, Mendel 
confirmed that he was using plants that bred true for white or violet flower 
color. Irrespective of the number of generations that Mendel examined, all 
self-crossed offspring of parents with white flowers had white flowers, and 
all self-crossed offspring of parents with violet flowers had violet flowers. 
In addition, Mendel confirmed that, other than flower color, the pea plants 
were physically identical. This was an important check to make sure that 
the two varieties of pea plants only differed with respect to one trait, flower 
color. 


Once these validations were complete, Mendel applied the pollen from a 
plant with violet flowers to the stigma of a plant with white flowers. After 
gathering and sowing the seeds that resulted from this cross, Mendel found 
that 100 percent of the F; hybrid generation had violet flowers. 
Conventional wisdom at that time would have predicted the hybrid flowers 
to be pale violet or for hybrid plants to have equal numbers of white and 
violet flowers. In other words, the contrasting parental traits were expected 
to blend in the offspring. Instead, Mendel’s results demonstrated that the 
white flower trait had completely disappeared in the F; generation. 


Importantly, Mendel did not stop his experimentation there. He allowed the 
F, plants to self-fertilize and found that 705 plants in the Fy generation had 
violet flowers and 224 had white flowers. This was a ratio of 3.15 violet 
flowers to one white flower, or approximately 3:1. When Mendel 
transferred pollen from a plant with violet flowers to the stigma of a plant 
with white flowers and vice versa, he obtained approximately the same ratio 
irrespective of which parent—male or female—contributed which trait. 


This is called a reciprocal cross —a paired cross in which the respective 
traits of the male and female in one cross become the respective traits of the 
female and male in the other cross. For the other six characteristics that 
Mendel examined, the F, and F> generations behaved in the same way that 
they behaved for flower color. One of the two traits would disappear 
completely from the F, generation, only to reappear in the F> generation at 
a ratio of roughly 3:1 ({link]). He wrote, in the typically sparse prose of a 
scientist, "In this generation, along with the dominating traits, the recessive 
ones also reappear, their individuality fully revealed, and they do so in the 
decisively expressed average proportion of 3:1, so that among each four 
plants of this generation three receive the dominating and one the recessive 
characteristic." (Gregor Mendel, 'Experiments on Plant Hybrids', 1865) 


Seed shape -) ae) 


Round Wrinkled 
Seed color ~) ww 
Flower position 
Yellow Green 
— - y 
Flower color ») (ob Axial Terminal 
Purple White 
Pod shape Jf J 
Inflated Constricted 
Stem height 
Pod color 
Yellow Green Tall Dwarf 


Mendel identified seven pea plant characteristics. 


Upon compiling his results for many thousands of plants, Mendel 
concluded that the characteristics could be divided into expressed and latent 
traits. He called these dominant and recessive traits, respectively. 
Dominant traits are those that are inherited unchanged in a hybridization. 
Recessive traits become latent, or disappear in the offspring of a 
hybridization. The recessive trait does, however, reappear in the progeny of 
the hybrid offspring. An example of a dominant trait is the violet-colored 
flower trait. For this same characteristic (flower color), white-colored 
flowers are a recessive trait. The fact that the recessive trait reappeared in 
the F> generation meant that the traits remained separate (and were not 
blended) in the plants of the F; generation. Mendel proposed that this was 
because the plants possessed two copies of the trait for the flower-color 
characteristic, and that each parent transmitted one of their two copies to 
their offspring, where they came together. Moreover, the physical 
observation of a dominant trait could mean that the genetic composition of 
the organism included two dominant versions of the characteristic, or that it 
included one dominant and one recessive version. Conversely, the 
observation of a recessive trait meant that the organism lacked any 
dominant versions of this characteristic. 


Laws of Inheritance 


Introduction 

"If A denotes one of the two constant traits, for example, the dominating 
one, a the recessive, and the Aa the hybrid form in which both are united, 
then the expression: A + 2Aa + a gives the series for the progeny of plants 
hybrid in a pair of differing traits. " Gregor Mendel, 1865 


The seven characteristics that Mendel evaluated in his pea plants were each 
expressed as one of two versions, or traits. Mendel deduced from his results 
that each individual had two discrete copies of the characteristic that are 
passed individually to offspring. We now call those two copies genes, which 
are carried on chromosomes. The reason we have two copies of each gene 
is that we inherit one from each parent. In fact, it is the chromosomes we 
inherit and the two copies of each gene are located on paired chromosomes. 
Recall that in meiosis these chromosomes are separated out into haploid 
gametes. This separation, or segregation, of the homologous chromosomes 
means also that only one of the copies of the gene gets moved into a 
gamete. The offspring are formed when that gamete unites with one from 
another parent and the two copies of each gene (and chromosome) are 
restored. 


For cases in which a single gene controls a single characteristic, a diploid 
organism has two genetic copies that may or may not encode the same 
version of that characteristic. For example, one individual may carry a gene 
that determines white flower color and a gene that determines violet flower 
color. Gene variants that arise by mutation and exist at the same relative 
locations on homologous chromosomes are called alleles. Mendel examined 
the inheritance of genes with just two allele forms, but it is common to 
encounter more than two alleles for any given gene in a natural population. 


Phenotypes and Genotypes 


Two alleles for a given gene in a diploid organism are expressed and 
interact to produce physical characteristics. The observable traits expressed 
by an organism are referred to as its phenotype. An organism’s underlying 
genetic makeup, consisting of both the physically visible and the non- 


expressed alleles, is called its genotype. Mendel’s hybridization 
experiments demonstrate the difference between phenotype and genotype. 
For example, the phenotypes that Mendel observed in his crosses between 
pea plants with differing traits are connected to the diploid genotypes of the 
plants in the P, F,, and F> generations. We will use a second trait that 
Mendel investigated, seed color, as an example. Seed color is governed by a 
single gene with two alleles. The yellow-seed allele is dominant and the 
green-seed allele is recessive. When true-breeding plants were cross- 
fertilized, in which one parent had yellow seeds and one had green seeds, 
all of the F; hybrid offspring had yellow seeds. That is, the hybrid offspring 
were phenotypically identical to the true-breeding parent with yellow seeds. 
However, we know that the allele donated by the parent with green seeds 
was not simply lost because it reappeared in some of the F> offspring 
({link]). Therefore, the F,; plants must have been genotypically different 
from the parent with yellow seeds. 


The P plants that Mendel used in his experiments were each homozygous 
for the trait he was studying. Diploid organisms that are homozygous for a 
gene have two identical alleles, one on each of their homologous 
chromosomes. The genotype is often written as YY or yy, for which each 
letter represents one of the two alleles in the genotype. The dominant allele 
is capitalized and the recessive allele is lower case. The letter used for the 
gene (seed color in this case) is usually related to the dominant trait (yellow 
allele, in this case, or “Y”). Mendel’s parental pea plants always bred true 
because both produced gametes carried the same allele. When P plants with 
contrasting traits were cross-fertilized, all of the offspring were 
heterozygous for the contrasting trait, meaning their genotype had different 
alleles for the gene being examined. For example, the F; yellow plants that 
received a Y allele from their yellow parent and a y allele from their green 
parent had the genotype Yy. 


Phenotype 


[P] at @ 
(a) Cross-fertilization 


: 
100 percent 
[Fa] 


yellow progeny 
(hybrids) 


.) 


y (b) Self-fertilization 


‘*) 75 percent 

© yellow 
progeny 
25 percent 


green 
progeny 


Genotype 


[Pp] yy “Ts YY 
(a) Cross-fertilization 


[F:] 


1 
00 ae (yellow) 


uv (b) Self-fertilization 


25 percent 
WAC 
(yellow) 


50 percent 
Yy 


25 percent 


y } (green) 


Phenotypes are physical expressions of traits that 
are transmitted by alleles. Capital letters represent 
dominant alleles and lowercase letters represent 
recessive alleles. The phenotypic ratios are the 
ratios of visible characteristics. The genotypic 
ratios are the ratios of gene combinations in the 
offspring, and these are not always distinguishable 
in the phenotypes. 


Law of Dominance 


Our discussion of homozygous and heterozygous organisms brings us to 
why the F, heterozygous offspring were identical to one of the parents, 
rather than expressing both alleles. In all seven pea-plant characteristics, 
one of the two contrasting alleles was dominant, and the other was 
recessive. Mendel called the dominant allele the expressed unit factor; the 
recessive allele was referred to as the latent unit factor. We now know that 
these so-called unit factors are actually genes on homologous 
chromosomes. For a gene that is expressed in a dominant and recessive 


pattern, homozygous dominant and heterozygous organisms will look 
identical (that is, they will have different genotypes but the same 
phenotype), and the recessive allele will only be observed in homozygous 
recessive individuals ({link]). 


Correspondence between Genotype and Phenotype for a 
Dominant-Recessive Characteristic. 


Homozygous Heterozygous Homozygous 
Genotype YY Yy yy 
Phenotype yellow yellow green 


Mendel’s law of dominance states that in a heterozygote, one trait will 
conceal the presence of another trait for the same characteristic. For 
example, when crossing true-breeding violet-flowered plants with true- 
breeding white-flowered plants, all of the offspring were violet-flowered, 
even though they all had one allele for violet and one allele for white. 
Rather than both alleles contributing to a phenotype, the dominant allele 
will be expressed exclusively. The recessive allele will remain latent, but 
will be transmitted to offspring in the same manner as that by which the 
dominant allele is transmitted. The recessive trait will only be expressed by 
offspring that have two copies of this allele ([link]), and these offspring will 
breed true when self-crossed. 


The allele for albinism, 
expressed here in humans, is 
recessive. Both of this 
child’s parents carried the 
recessive allele. 


Monohybrid Cross and the Punnett Square 


When fertilization occurs between two true-breeding parents that differ by 
only the characteristic being studied, the process is called a monohybrid 
cross, and the resulting offspring are called monohybrids. Mendel 
performed seven types of monohybrid crosses, each involving contrasting 
traits for different characteristics. Out of these crosses, all of the F, 
offspring had the phenotype of one parent, and the F> offspring had a 3:1 
phenotypic ratio. On the basis of these results, Mendel postulated that each 
parent in the monohybrid cross contributed one of two paired unit factors to 
each offspring, and every possible combination of unit factors was equally 
likely. 


The results of Mendel’s research can be explained in terms of probabilities, 
which are mathematical measures of likelihood. The probability of an event 
is calculated by the number of times the event occurs divided by the total 
number of opportunities for the event to occur. A probability of one (100 
percent) for some event indicates that it is guaranteed to occur, whereas a 
probability of zero (0 percent) indicates that it is guaranteed to not occur, 
and a probability of 0.5 (50 percent) means it has an equal chance of 
occurring or not occurring. 


To demonstrate this with a monohybrid cross, consider the case of true- 
breeding pea plants with yellow versus green seeds. The dominant seed 
color is yellow; therefore, the parental genotypes were YY for the plants 
with yellow seeds and yy for the plants with green seeds. A Punnett 
square, devised by the British geneticist Reginald Punnett, is useful for 
determining probabilities because it is drawn to predict all possible 
outcomes of all possible random fertilization events and their expected 
frequencies. [link] shows a Punnett square for a cross between a plant with 
yellow peas and one with green peas. To prepare a Punnett square, all 
possible combinations of the parental alleles (the genotypes of the gametes) 
are listed along the top (for one parent) and side (for the other parent) of a 
grid. The combinations of egg and sperm gametes are then made in the 
boxes in the table on the basis of which alleles are combining. Each box 
then represents the diploid genotype of a zygote, or fertilized egg. Because 
each possibility is equally likely, genotypic ratios can be determined from a 
Punnett square. If the pattern of inheritance (dominant and recessive) is 
known, the phenotypic ratios can be inferred as well. For a monohybrid 
cross of two true-breeding parents, each parent contributes one type of 
allele. In this case, only one genotype is possible in the F, offspring. All 
offspring are Yy and have yellow seeds. 


When the F, offspring are crossed with each other, each has an equal 
probability of contributing either a Y or a y to the F, offspring. The result is 
a 1 in 4 (25 percent) probability of both parents contributing a Y, resulting 
in an offspring with a yellow phenotype; a 25 percent probability of parent 
A contributing a Y and parent B ay, resulting in offspring with a yellow 
phenotype; a 25 percent probability of parent A contributing a y and parent 
B a, also resulting in a yellow phenotype; and a (25 percent) probability 


of both parents contributing a y, resulting in a green phenotype. When 
counting all four possible outcomes, there is a 3 in 4 probability of offspring 
having the yellow phenotype and a 1 in 4 probability of offspring having 
the green phenotype. This explains why the results of Mendel’s F> 
generation occurred in a 3:1 phenotypic ratio. Using large numbers of 
crosses, Mendel was able to calculate probabilities, found that they fit the 
model of inheritance, and use these to predict the outcomes of other crosses. 


Law of Segregation 


Observing that true-breeding pea plants with contrasting traits gave rise to 
F, generations that all expressed the dominant trait and F> generations that 
expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed 
the law of segregation. This law states that paired unit factors (genes) must 
segregate equally into gametes such that offspring have an equal likelihood 
of inheriting either factor. For the F> generation of a monohybrid cross, the 
following three possible combinations of genotypes result: homozygous 
dominant, heterozygous, or homozygous recessive. Because heterozygotes 
could arise from two different pathways (receiving one dominant and one 
recessive allele from either parent), and because heterozygotes and 
homozygous dominant individuals are phenotypically identical, the law 
supports Mendel’s observed 3:1 phenotypic ratio. The equal segregation of 
alleles is the reason we can apply the Punnett square to accurately predict 
the offspring of parents with known genotypes. The physical basis of 
Mendel’s law of segregation is the first division of meiosis in which the 
homologous chromosomes with their different versions of each gene are 
segregated into daughter nuclei. This process was not understood by the 
scientific community during Mendel’s lifetime ([link]). 


Meiosis | Daughter 
cells 


Interphase Prometaphase | Anaphase | 


Prophase | Metaphase | Telophase | 


The first division in meiosis is shown. 


Test Cross 


Beyond predicting the offspring of a cross between known homozygous or 
heterozygous parents, Mendel also developed a way to determine whether 
an organism that expressed a dominant trait was a heterozygote or a 
homozygote. Called the test cross, this technique is still used by plant and 
animal breeders. In a test cross, the dominant-expressing organism is 
crossed with an organism that is homozygous recessive for the same 
characteristic. If the dominant-expressing organism is a homozygote, then 
all F, offspring will be heterozygotes expressing the dominant trait ({link]). 
Alternatively, if the dominant-expressing organism is a heterozygote, the F; 
offspring will exhibit a 1:1 ratio of heterozygotes and recessive 
homozygotes ([link]). The test cross further validates Mendel’s postulate 
that pairs of unit factors segregate equally. 


Note: 


A test cross can be performed to 
determine whether an organism 
expressing a dominant trait is a 
homozygote or a heterozygote. 


Genotype Phenotype 
Phenotypes Genotypes ratio ratio 


This Punnett square shows the cross 
between plants with yellow seeds and 
green seeds. The cross between the 
true-breeding P plants produces F, 
heterozygotes that can be self- 
fertilized. The self-cross of the F, 
generation can be analyzed with a 
Punnett square to predict the 
genotypes of the F, generation. Given 
an inheritance pattern of dominant— 
recessive, the genotypic and 
phenotypic ratios can then be 
determined. 


Law of Independent Assortment 


Mendel’s law of independent assortment states that genes do not 
influence each other with regard to the sorting of alleles into gametes, and 
every possible combination of alleles for every gene is equally likely to 
occur. Independent assortment of genes can be illustrated by the dihybrid 
cross, a cross between two true-breeding parents that express different traits 
for two characteristics. Consider the characteristics of seed color and seed 
texture for two pea plants, one that has wrinkled, green seeds (rryy) and 
another that has round, yellow seeds (RRYY). Because each parent is 
homozygous, the law of segregation indicates that the gametes for the 
wrinkled—green plant all are ry, and the gametes for the round—yellow plant 
are all RY. Therefore, the F, generation of offspring all are RrYy ([link)). 


Note: 


A dihybrid cross in pea plants involves the genes 
for seed color and texture. The P cross produces 
F, offspring that are all heterozygous for both 
characteristics. The resulting 9:3:3:1 F> 
phenotypic ratio is obtained using a Punnett 
square. 


The gametes produced by the F individuals must have one allele from each 
of the two genes. For example, a gamete could get an R allele for the seed 
shape gene and either a Y or ay allele for the seed color gene. It cannot get 
both an R and an r allele; each gamete can have only one allele per gene. 
The law of independent assortment states that a gamete into which an r 
allele is sorted would be equally likely to contain either a Y or ay allele. 
Thus, there are four equally likely gametes that can be formed when the 
RrYy heterozygote is self-crossed, as follows: RY, rY, Ry, and ry. Arranging 


these gametes along the top and left of a 4 x 4 Punnett square ([link]) gives 
us 16 equally likely genotypic combinations. From these genotypes, we find 
a phenotypic ratio of 9 round—yellow:3 round—green:3 wrinkled—yellow:1 
wrinkled—green ([{link]). These are the offspring ratios we would expect, 
assuming we performed the crosses with a large enough sample size. 


The physical basis for the law of independent assortment also lies in 
meiosis I, in which the different homologous pairs line up in random 
orientations. Each gamete can contain any combination of paternal and 
maternal chromosomes (and therefore the genes on them) because the 
orientation of tetrads on the metaphase plane is random ([link]). 


Metaphase | _ 


Metaphase II 


Gametes 


i 
a 
: 
: 
a 
: 
iS 
é 


Metaphase II 


Chromosome Arrangement 2 


© Gametes © 
Genetic Genetic 
arrangement 3 arrangement 4 


The random segregation into daughter nuclei that 
happens during the first division in meiosis can lead to a 
variety of possible genetic arrangements. 


Extensions of the Laws of Inheritance 


Introduction 

"Certain students of genetics inferred that the Mendelian units responsible 
for the selected character were genes producing only a single effect. This 
was careless logic. It took a good deal of hammering to get rid of this 
erroneous idea. As facts accumulated it became evident that each gene 
produces not a single effect, but in some cases a multitude of effects on the 
characters of the individual. It is true that in most genetic work only one of 
these character-effects is selected for study—the one that is most sharply 
defined and separable from its contrasted character—but in most cases 
minor differences also are recognizable that are just as much the product of 
the same gene as is the major effect. " Thomas Hunt Morgan, 1935 


Mendel studied traits with only one mode of inheritance, and one very 
obvious phenotype, in pea plants. The inheritance of the traits he studied all 
followed the relatively simple pattern of dominant and recessive alleles for 
a single characteristic, and allowed him to suggest his Laws of Inheritance. 
There are several important modes of inheritance, discovered after 
Mendel’s work, that do not follow the dominant and recessive, single-gene 
model. So mendel's Laws are not always going to predict the phenotypes 
seen after doing a genetic cross. 


Alternatives to Dominance and Recessiveness 


Mendel’s experiments with pea plants suggested that: 1) two types of 
“units” or alleles exist for every gene; 2) alleles maintain their integrity in 
each generation (no blending); and 3) in the presence of the dominant allele, 
the recessive allele is hidden, with no contribution to the phenotype. 
Therefore, recessive alleles can be “carried” and not expressed by 
individuals. Such heterozygous individuals are sometimes referred to as 
“carriers.” Since then, genetic studies in other organisms have shown that 
much more complexity exists, but that the fundamental principles of 
Mendelian genetics still hold true. In the sections to follow, we consider 
some of the extensions of Mendelism. 


Incomplete Dominance 


Mendel’s results, demonstrating that traits are inherited as dominant and 
recessive pairs, contradicted the view at that time that offspring exhibited a 
blend of their parents’ traits. However, the heterozygote phenotype 
occasionally does appear to be intermediate between the two parents. For 
example, in the snapdragon, Antirrhinum majus ({link]), a cross between a 
homozygous parent with white flowers (C’C™) and a homozygous parent 
with red flowers (CC®) will produce offspring with pink flowers (C®C). 
(Note that different genotypic abbreviations are used for Mendelian 
extensions to distinguish these patterns from simple dominance and 
recessiveness.) This pattern of inheritance is described as incomplete 
dominance, meaning that one of the alleles appears in the phenotype in the 
heterozygote, but not to the exclusion of the other, which can also be seen. 
The allele for red flowers is incompletely dominant over the allele for white 
flowers. However, the results of a heterozygote self-cross can still be 
predicted, just as with Mendelian dominant and recessive crosses. In this 
case, the genotypic ratio would be 1 CRC:2 CRCW:1 CYC", and the 
phenotypic ratio would be 1:2:1 for red:pink:white. The basis for the 
intermediate color in the heterozygote is simply that the pigment produced 
by the red allele (anthocyanin) is diluted in the heterozygote and therefore 
appears pink because of the white background of the flower petals. 


These pink flowers of a 
heterozygote snapdragon 
result from incomplete 
dominance. (credit: 
"storebukkebruse"/Flickr) 


Codominance 


A variation on incomplete dominance is codominance, in which both 
alleles for the same characteristic are simultaneously expressed in the 
heterozygote. An example of codominance occurs in the ABO blood groups 
of humans. The A and B alleles are expressed in the form of A or B 
molecules present on the surface of red blood cells. Homozygotes (I4I4 and 
1°18) express either the A or the B phenotype, and heterozygotes (I“I°) 
express both phenotypes equally. The /4/8 individual has blood type AB. In 
a self-cross between heterozygotes expressing a codominant trait, the three 


possible offspring genotypes are phenotypically distinct. However, the 1:2:1 
genotypic ratio characteristic of a Mendelian monohybrid cross still applies 
((link]). 


Codominant Cross 


Genotypes Genotype ratio 


This Punnet square shows an AB/AB 
blood type cross 


Multiple Alleles 


Mendel implied that only two alleles, one dominant and one recessive, 
could exist for a given gene. We now know that this is an 
oversimplification. Although individual humans (and all diploid organisms) 
can only have two alleles for a given gene, multiple alleles may exist at the 
population level, such that many combinations of two alleles are observed. 
Note that when many alleles exist for the same gene, the convention is to 


denote the most common phenotype or genotype in the natural population 
as the wild type (often abbreviated “+”). All other phenotypes or genotypes 
are considered variants (mutants) of this typical form, meaning they deviate 
from the wild type. The variant may be recessive or dominant to the wild- 
type allele. 


An example of multiple alleles is the ABO blood-type system in humans. In 
this case, there are three alleles circulating in the population. The J“ allele 
codes for A molecules on the red blood cells, the I? allele codes for B 
molecules on the surface of red blood cells, and the i allele codes for no 
molecules on the red blood cells. In this case, the [4 and I? alleles are 
codominant with each other and are both dominant over the i allele. 
Although there are three alleles present in a population, each individual 
only gets two of the alleles from their parents. This produces the genotypes 
and phenotypes shown in [link]. Notice that instead of three genotypes, 
there are six different genotypes when there are three alleles. The number of 
possible phenotypes depends on the dominance relationships between the 
three alleles. 


Inheritance of the ABO Blood System in Humans 


Inheritance of the ABO blood system in 
humans is shown. 


Note: 

Evolution in Action 

Multiple Alleles Confer Drug Resistance in the Malaria Parasite 
Malaria is a parasitic disease in humans that is transmitted by infected 
female mosquitoes, including Anopheles gambiae, and is characterized by 
cyclic high fevers, chills, flu-like symptoms, and severe anemia. 
Plasmodium falciparum and P. vivax are the most common causative 
agents of malaria, and P. falciparum is the most deadly. When promptly 
and correctly treated, P. falciparum malaria has a mortality rate of 0.1 
percent. However, in some parts of the world, the parasite has evolved 
resistance to commonly used malaria treatments, so the most effective 
malarial treatments can vary by geographic region. 

In Southeast Asia, Africa, and South America, P. falciparum has developed 
resistance to the anti-malarial drugs chloroquine, mefloquine, and 
sulfadoxine-pyrimethamine. P. falciparum, which is haploid during the life 
stage in which it is infective to humans, has evolved multiple drug-resistant 
mutant alleles of the dhps gene. Varying degrees of sulfadoxine resistance 
are associated with each of these alleles. Being haploid, P. falciparum 
needs only one drug-resistant allele to express this trait. 

In Southeast Asia, different sulfadoxine-resistant alleles of the dhps gene 
are localized to different geographic regions. This is a common 
evolutionary phenomenon that comes about because drug-resistant mutants 
arise in a population and interbreed with other P. falciparum isolates in 
close proximity. Sulfadoxine-resistant parasites cause considerable human 
hardship in regions in which this drug is widely used as an over-the- 
counter malaria remedy. As is common with pathogens that multiply to 
large numbers within an infection cycle, P. falciparum evolves relatively 
rapidly (over a decade or so) in response to the selective pressure of 
commonly used anti-malarial drugs. For this reason, scientists must 
constantly work to develop new drugs or drug combinations to combat the 
worldwide malaria burden. |{otmote! 

Sumiti Vinayak et al., “Origin and Evolution of Sulfadoxine Resistant 
Plasmodium falciparum,” PLoS Pathogens 6 (2010): e1000830. 


Sex-Linked Traits 


In humans, as well as in many other animals and some plants, the sex of the 
individual is determined by sex chromosomes—one pair of non- 
homologous chromosomes. Until now, we have only considered inheritance 
patterns among non-sex chromosomes, or autosomes. In addition to 22 
homologous pairs of autosomes, human females have a homologous pair of 
X chromosomes, whereas human males have an XY chromosome pair. 
Although the Y chromosome contains a small region of similarity to the X 
chromosome so that they can pair during meiosis, the Y chromosome is 
much shorter and contains fewer genes. When a gene being examined is 
present on the X, but not the Y, chromosome, it is X-linked. 


Eye color in Drosophila, the common fruit fly, was the first X-linked trait to 
be identified. Thomas Hunt Morgan mapped this trait to the X chromosome 
in 1910. Like humans, Drosophila males have an XY chromosome pair, and 
females are XX. In flies the wild-type eye color is red (X”) and is dominant 
to white eye color (X™) ([link]). Because of the location of the eye-color 
gene, reciprocal crosses do not produce the same offspring ratios. Males are 
said to be hemizygous, in that they have only one allele for any X-linked 
characteristic. Hemizygosity makes descriptions of dominance and 
recessiveness irrelevant for XY males. Drosophila males lack the white 
gene on the Y chromosome; that is, their genotype can only be XWY or 
XY. In contrast, females have two allele copies of this gene and can be 
KOK XK Or KX, 


In Drosophila, the gene for eye color 

is located on the X chromosome. Red 

eye color is wild-type and is dominant 
to white eye color. 


In an X-linked cross, the genotypes of F, and F, offspring depend on 
whether the recessive trait was expressed by the male or the female in the P 
generation. With respect to Drosophila eye color, when the P male 
expresses the white-eye phenotype and the female is homozygously red- 
eyed, all members of the F; generation exhibit red eyes ([link]). The F; 
females are heterozygous (X“X”), and the males are all XY, having 
received their X chromosome from the homozygous dominant P female and 
their Y chromosome from the P male. A subsequent cross between the 
XX” female and the X”Y male would produce only red-eyed females 
(with X“X™ or X“X™ genotypes) and both red- and white-eyed males (with 
XWY or X”Y genotypes). Now, consider a cross between a homozygous 
white-eyed female and a male with red eyes. The F; generation would 
exhibit only heterozygous red-eyed females (X“X”) and only white-eyed 
males (X“Y). Half of the F, females would be red-eyed (XX) and half 
would be white-eyed (X“X™). Similarly, half of the F, males would be red- 
eyed (XY) and half would be white-eyed (X“Y). 


Note: 


Punnett Square Analysis of a Sex-linked Trait 


All female offspring 
have red eyes. 


All male offspring 
have white eyes. 


Crosses involving sex-linked traits often 
give rise to different phenotypes for the 
different sexes of offspring, as is the case for 
this cross involving red and white eye color 
in Drosophila. In the diagram, w is the 
white-eye mutant allele and W is the wild- 
type, red-eye allele. 


Discoveries in fruit fly genetics can be applied to human genetics. When a 
female parent is homozygous for a recessive X-linked trait, she will pass the 
trait on to 100 percent of her male offspring, because the males will receive 
the Y chromosome from the male parent. In humans, the alleles for certain 
conditions (some color-blindness, hemophilia, and muscular dystrophy) are 


X-linked. Females who are heterozygous for these diseases are said to be 
carriers and may not exhibit any phenotypic effects. These females will pass 
the disease to half of their sons and will pass carrier status to half of their 
daughters; therefore, X-linked traits appear more frequently in males than 
females. 


In some groups of organisms with sex chromosomes, the sex with the non- 
homologous sex chromosomes is the female rather than the male. This is 
the case for all birds. In this case, sex-linked traits will be more likely to 
appear in the female, in whom they are hemizygous. 


Linked Genes Violate the Law of Independent Assortment 


Although all of Mendel’s pea plant characteristics behaved according to the 
law of independent assortment, we now know that some allele combinations 
are not inherited independently of each other. Genes that are located on 
separate, non-homologous chromosomes will always sort independently. 
However, each chromosome contains hundreds or thousands of genes, 
organized linearly on chromosomes like beads on a string. The segregation 
of alleles into gametes can be influenced by linkage, in which genes that 
are located physically close to each other on the same chromosome are 
more likely to be inherited as a pair. However, because of the process of 
recombination, or “crossover,” it is possible for two genes on the same 
chromosome to behave independently, or as if they are not linked. To 
understand this, let us consider the biological basis of gene linkage and 
recombination. 


Homologous chromosomes possess the same genes in the same order, 
though the specific alleles of the gene can be different on each of the two 
chromosomes. Recall that during interphase and prophase I of meiosis, 
homologous chromosomes first replicate and then synapse, with like genes 
on the homologs aligning with each other. At this stage, segments of 
homologous chromosomes exchange linear segments of genetic material 
({link]). This process is called recombination, or crossover, and it is a 
common genetic process. Because the genes are aligned during 
recombination, the gene order is not altered. Instead, the result of 
recombination is that maternal and paternal alleles are combined onto the 


same chromosome. Across a given chromosome, several recombination 
events may occur, causing extensive shuffling of alleles. 


Homologous Chromosome Recombinant 
chromosomes crossover chromosomes 
aligned 


Non-recombinant 
chromosomes 


The process of crossover, or recombination, occurs 
when two homologous chromosomes align and 
exchange a segment of genetic material. 


When two genes are located on the same chromosome, they are considered 
linked, and their alleles tend to be transmitted through meiosis together. To 
exemplify this, imagine a dihybrid cross involving flower color and plant 
height in which the genes are next to each other on the chromosome. If one 
homologous chromosome has alleles for tall plants and red flowers, and the 
other chromosome has genes for short plants and yellow flowers, then when 
the gametes are formed, the tall and red alleles will tend to go together into 
a gamete and the short and yellow alleles will go into other gametes. These 
are called the parental genotypes because they have been inherited intact 
from the parents of the individual producing gametes. But unlike if the 
genes were on different chromosomes, there will be no gametes with tall 
and yellow alleles and no gametes with short and red alleles. If you create a 
Punnett square with these gametes, you will see that the classical Mendelian 
prediction of a 9:3:3:1 outcome of a dihybrid cross would not apply. As the 


distance between two genes increases, the probability of one or more 
crossovers between them increases and the genes behave more like they are 
on separate chromosomes. Geneticists have used the proportion of 
recombinant gametes (the ones not like the parents) as a measure of how far 
apart genes are on a chromosome. Using this information, they have 
constructed linkage maps of genes on chromosomes for well-studied 
organisms, including humans. 


Mendel’s seminal publication makes no mention of linkage, and many 
researchers have questioned whether he encountered linkage but chose not 
to publish those crosses out of concern that they would invalidate his 
independent assortment postulate. The garden pea has seven chromosomes, 
and some have suggested that his choice of seven characteristics was not a 
coincidence. However, even if the genes he examined were not located on 
separate chromosomes, it is possible that he simply did not observe linkage 
because of the extensive shuffling effects of recombination. 


Population Evolution 


Introduction 

"Genetics is to biology what atomic theory is to physics. Its principle is 
clear: that inheritance is based on particles and not on fluids. Instead of the 
essence of each parent mixing, with each child the blend of those who made 
him, information is passed on as a Series of units. The bodies of successive 
generations transport them through time, so that a long-lost character may 
emerge in a distant descendant. The genes themselves may be older than the 
species that bear them." — John Stephen Jones, Almost Like a Whale: The 
Origin of Species Updated. Doubleday, 1999. 


The mechanisms of inheritance, or genetics, were not understood at the time 
Charles Darwin and Alfred Russel Wallace were developing their idea of 
natural selection. This lack of understanding was a stumbling block to 
understanding many aspects of evolution. In fact, the predominant (and 
incorrect) genetic theory of the time, blending inheritance, made it difficult 
to understand how natural selection might operate. Darwin and Wallace 
were unaware of the genetics work by Austrian monk Gregor Mendel, 
which was published in 1866, not long after publication of Darwin's book, 
On the Origin of Species. Mendel’s work was rediscovered in the early 
twentieth century at which time geneticists were rapidly coming to an 
understanding of the basics of inheritance. Initially, the newly discovered 
particulate nature of genes made it difficult for biologists to understand how 
gradual evolution could occur. But over the next few decades genetics and 
evolution were integrated in what became known as the modern synthesis 
—the coherent understanding of the relationship between natural selection 
and genetics that took shape by the 1940s and is generally accepted today. 
In sum, the modern synthesis describes how evolutionary processes, such as 
natural selection, can affect a population’s genetic makeup, and, in turn, 
how this can result in the gradual evolution of populations and species. The 
theory also connects this change of a population over time, called 
microevolution, with the processes that gave rise to new species and higher 
taxonomic groups with widely divergent characters, called 
macroevolution. 


Note: 

Evolution and Flu Vaccines 

Every fall, the media starts reporting on flu vaccinations and potential 
outbreaks. Scientists, health experts, and institutions determine 
recommendations for different parts of the population, predict optimal 
production and inoculation schedules, create vaccines, and set up clinics to 
provide inoculations. You may think of the annual flu shot as a lot of media 
hype, an important health protection, or just a briefly uncomfortable prick 
in your arm. But do you think of it in terms of evolution? 

The media hype of annual flu shots is scientifically grounded in our 
understanding of evolution. Each year, scientists across the globe strive to 
predict the flu strains that they anticipate being most widespread and 
harmful in the coming year. This knowledge is based in how flu strains 
have evolved over time and over the past few flu seasons. Scientists then 
work to create the most effective vaccine to combat those selected strains. 
Hundreds of millions of doses are produced in a short period in order to 
provide vaccinations to key populations at the optimal time. 

Because viruses, like the flu, evolve very quickly (especially in 
evolutionary time), this poses quite a challenge. Viruses mutate and 
replicate at a fast rate, so the vaccine developed to protect against last 
year’s flu strain may not provide the protection needed against the coming 
year’s strain. Evolution of these viruses means continued adaptions to 
ensure survival, including adaptations to survive previous vaccines. 


Population Genetics 


Recall that a gene for a particular character may have several alleles, or 
variants, that code for different traits associated with that character. For 
example, in the ABO blood type system in humans, three alleles determine 
the particular blood-type protein on the surface of red blood cells. Each 
individual in a population of diploid organisms can only carry two alleles 
for a particular gene, but more than two may be present in the individuals 
that make up the population. Mendel followed alleles as they were inherited 
from parent to offspring. In the early twentieth century, biologists in a field 


of study known as population genetics began to study how selective forces 
change a population through changes in allele and genotypic frequencies. 


The allele frequency (or gene frequency) is the rate at which a specific 
allele appears within a population. Until now we have discussed evolution 
as a change in the characteristics of a population of organisms, but behind 
that phenotypic change is genetic change. In population genetics, the term 
evolution is defined as a change in the frequency of an allele in a 
population. Using the ABO blood type system as an example, the frequency 
of one of the alleles, I“, is the number of copies of that allele divided by all 
the copies of the ABO gene in the population. For example, a study in 
Jordan!2mote] found a frequency of I“ to be 26.1 percent. The I® and [° 
alleles made up 13.4 percent and 60.5 percent of the alleles respectively, 
and all of the frequencies added up to 100 percent. A change in this 
frequency over time would constitute evolution in the population. 

Sahar S. Hanania, Dhia S. Hassawi, and Nidal M. Irshaid, “Allele 
Frequency and Molecular Genotypes of ABO Blood Group System in a 
Jordanian Population,” Journal of Medical Sciences 7 (2007): 51-58, 

doi: 10.3923/jms.2007.51.58. 


The allele frequency within a given population can change depending on 
environmental factors; therefore, certain alleles become more widespread 
than others during the process of natural selection. Natural selection can 
alter the population’s genetic makeup; for example, if a given allele confers 
a phenotype that allows an individual to better survive or have more 
offspring. Because many of those offspring will also carry the beneficial 
allele, and often the corresponding phenotype, they will have more 
offspring of their own that also carry the allele, thus, perpetuating the cycle. 
Over time, the allele will spread throughout the population. Some alleles 
will quickly become fixed in this way, meaning that every individual of the 
population will carry the allele, while detrimental mutations may be swiftly 
eliminated if derived from a dominant allele from the gene pool. The gene 
pool is the sum of all the alleles in a population. 


Sometimes, allele frequencies within a population change randomly with no 
advantage to the population over existing allele frequencies. This 
phenomenon is called genetic drift. Natural selection and genetic drift 


usually occur simultaneously in populations and are not isolated events. It is 
hard to determine which process dominates because it is often nearly 
impossible to determine the cause of change in allele frequencies at each 
occurrence. An event that initiates an allele frequency change in an isolated 
part of the population, which is not typical of the original population, is 
called the founder effect. Natural selection, random drift, and founder 
effects can lead to significant changes in the genome of a population. 


Hardy-Weinberg Principle of Equilibrium 


In the early twentieth century, English mathematician Godfrey Hardy and 
German physician Wilhelm Weinberg stated the principle of equilibrium to 
describe the genetic makeup of a population. The theory, which later 
became known as the Hardy-Weinberg principle of equilibrium, states 
that a population’s allele and genotype frequencies are inherently stable— 
unless some kind of evolutionary force is acting upon the population, 
neither the allele nor the genotypic frequencies would change. The Hardy- 
Weinberg principle assumes conditions with no mutations, migration, 
emigration, or selective pressure for or against genotype, plus an infinite 
population; while no population can satisfy those conditions, the principle 
offers a useful model against which to compare real population changes. 


Working under this theory, population geneticists represent different alleles 
as different variables in their mathematical models. The variable p, for 
example, often represents the frequency of a particular allele, say Y for the 
trait of yellow in Mendel’s peas, while the variable q represents the 
frequency of y alleles that confer the color green. If these are the only two 
possible alleles for a given locus in the population, p + gq = 1. In other 
words, all the p alleles and all the g alleles make up all of the alleles for that 
locus that are found in the population. 


But what ultimately interests most biologists is not the frequencies of 
different alleles, but the frequencies of the resulting genotypes, known as 
the population’s genetic structure, from which scientists can surmise the 
distribution of phenotypes. If the phenotype is observed, only the genotype 
of the homozygous recessive alleles can be known; the calculations provide 
an estimate of the remaining genotypes. Since each individual carries two 


alleles per gene, if the allele frequencies (p and q) are known, predicting the 
frequencies of these genotypes is a simple mathematical calculation to 
determine the probability of getting these genotypes if two alleles are drawn 
at random from the gene pool. So in the above scenario, an individual pea 
plant could be pp (YY), and thus produce yellow peas; pq (Yy), also 
yellow; or qq (yy), and thus producing green peas ([link]). In other words, 
the frequency of pp individuals is simply p?; the frequency of pq 
individuals is 2pq; and the frequency of qq individuals is q?. And, again, if 
p and q are the only two possible alleles for a given trait in the population, 
these genotypes frequencies will sum to one: p* + 2pq + q? = 1. 


Note: 


Hardy-Weinberg Principle 


Parent generation 
Phenotype 
Genotypic frequency 


Number of individuals 
(total = 500) 


Number of alleles Y: 490 + 210 = 700 
in gene pool 
(total = 1000) gy 


TALON 300 y 
Allelic frequency 1000 total ~~ 


7=p 7000 total — “2-9 


Hardy-Weinberg p (.7) q (.3) 
analysis 


2(.7)(.3) 


8 


Predicted Predicted Predicted 
frequency frequency frequency 
of YY of Yy of yy 
offspring offspring offspring 


When populations are in the Hardy-Weinberg 
equilibrium, the allelic frequency is stable from 
generation to generation and the distribution of 

alleles can be determined from the Hardy- 
Weinberg equation. If the allelic frequency 
measured in the field differs from the predicted 
value, scientists can make inferences about what 
evolutionary forces are at play. 


In theory, if a population is at equilibrium—that is, there are no 
evolutionary forces acting upon it—generation after generation would have 
the same gene pool and genetic structure, and these equations would all 
hold true all of the time. Of course, even Hardy and Weinberg recognized 
that no natural population is immune to evolution. Populations in nature are 
constantly changing in genetic makeup due to drift, mutation, possibly 
migration, and selection. As a result, the only way to determine the exact 
distribution of phenotypes in a population is to go out and count them. But 
the Hardy-Weinberg principle gives scientists a mathematical baseline of a 
non-evolving population to which they can compare evolving populations 
and thereby infer what evolutionary forces might be at play. If the 
frequencies of alleles or genotypes deviate from the value expected from 
the Hardy-Weinberg equation, then the population is evolving. 


Population Genetics 


Introduction 

" The proof given by Wright, that non-adaptive differentiation will occur in 
small populations owing to ‘drift’, or the chance fixation of some new 
mutation or recombination, is one of the most important results of 
mathematical analysis applied to the facts of neo-mendelism. It gives 
accident as well as adaptation a place in evolution, and at one stroke 
explains many facts which puzzled earlier selectionists, notably the much 
greater degree of divergence shown by island than mainland forms, by 
forms in isolated lakes than in continuous river-systems. " Sir Julian 
Huxley, 1942 


The leap from understanding genes and mutations to an understanding of 
the evolution of populations required the identification of other mechanisms 
that allowed genes to become common or uncommon in populations. 
Individuals of a population often display different phenotypes, or express 
different alleles of a particular gene, referred to as polymorphisms. 
Populations with two or more variations of particular characteristics are 
called polymorphic. The distribution of phenotypes among individuals, 
known as the population variation, is influenced by a number of factors, 
including the population’s genetic structure and the environment ((link]). 
Understanding the sources of a phenotypic variation in a population is 
important for determining how a population will evolve in response to 
different evolutionary pressures. 


The distribution of phenotypes in this 


litter of kittens illustrates population 
variation. (credit: Pieter Lanser) 


Genetic Variance 


Natural selection and some of the other evolutionary forces can only act on 
heritable traits, namely an organism’s genetic code. Because alleles are 
passed from parent to offspring, those that confer beneficial traits or 
behaviors may be selected for, while deleterious alleles may be selected 
against. Acquired traits, for the most part, are not heritable. For example, if 
an athlete works out in the gym every day, building up muscle strength, the 
athlete’s offspring will not necessarily grow up to be a body builder. If there 
is a genetic basis for the ability to run fast, on the other hand, this may be 
passed to a child. 


Heritability is the fraction of phenotype variation that can be attributed to 
genetic differences, or genetic variance, among individuals in a population. 
The greater the hereditability of a population’s phenotypic variation, the 
more susceptible it is to the evolutionary forces that act on heritable 
variation. 


The diversity of alleles and genotypes within a population is called genetic 
variance. When scientists are involved in the breeding of a species, such as 
with animals in zoos and nature preserves, they try to increase a 
population’s genetic variance to preserve as much of the phenotypic 
diversity as they can. This also helps reduce the risks associated with 
inbreeding, the mating of closely related individuals, which can have the 
undesirable effect of bringing together deleterious recessive mutations that 
can cause abnormalities and susceptibility to disease. For example, a 
disease that is caused by a rare, recessive allele might exist in a population, 
but it will only manifest itself when an individual carries two copies of the 
allele. Because the allele is rare in a normal, healthy population with 
unrestricted habitat, the chance that two carriers will mate is low, and even 
then, only 25 percent of their offspring will inherit the disease allele from 
both parents. While it is likely to happen at some point, it will not happen 


frequently enough for natural selection to be able to swiftly eliminate the 
allele from the population, and as a result, the allele will be maintained at 
low levels in the gene pool. However, if a family of carriers begins to 
interbreed with each other, this will dramatically increase the likelihood of 
two carriers mating and eventually producing diseased offspring, a 
phenomenon known as inbreeding depression. 


Changes in allele frequencies that are identified in a population can shed 
light on how it is evolving. In addition to natural selection, there are other 
evolutionary forces that could be in play: natural selection, genetic drift, 
gene flow, mutation, and nonrandom mating. 


Natural Selection 


The theory of natural selection stems from the observation that some 
individuals in a population are more likely to survive longer and have more 
offspring than others; thus, they will pass on more of their genes to the next 
generation. A big, powerful male gorilla, for example, is much more likely 
than a smaller, weaker one to become the population’s silverback, the 
pack’s leader who mates far more than the other males of the group. The 
pack leader will father more offspring, who share half of his genes, and are 
likely to also grow bigger and stronger like their father. Over time, the 
genes for bigger size will increase in frequency in the population, and the 
population will, as a result, grow larger on average. That is, this would 
occur if this particular selection pressure, or driving selective force, were 
the only one acting on the population. In other examples, better camouflage 
or a stronger resistance to drought might pose a selection pressure. 


Genetic Drift 


Another way a population’s allele and genotype frequencies can change is 
genetic drift ({link]), which is simply the effect of chance. By chance, 
some individuals will have more offspring than others—not due to an 
advantage conferred by some genetically-encoded trait, but just because one 
male happened to be in the right place at the right time (when the receptive 
female walked by) or because the other one happened to be in the wrong 
place at the wrong time (when a fox was hunting). 


Note: 


First generation 
p (B allele frequency) = .5 
p (B allele frequency) =.5 


5 rabbits reproduce 


Second generation 
p (B allele frequency) = .7 
p (B allele frequency) = .3 


dddd. 
G0. 0. a. @. 


2 rabbits reproduce | 


Third generation 
p (B allele frequency) =1 
p (B allele frequency) =0 


@.¢.@.¢. @. 
@.d.¢. ¢. @. 


Genetic drift in a population 
can lead to the elimination of 
an allele from a population 
by chance. In this example, 
rabbits with the brown coat 
color allele (B) are dominant 
over rabbits with the white 
coat color allele (b). In the 
first generation, the two 
alleles occur with equal 


frequency in the population, 
resulting in p and q values of 
.o. Only half of the 
individuals reproduce, 
resulting in a second 
generation with p and q 
values of .7 and .3, 
respectively. Only two 
individuals in the second 
generation reproduce, and by 
chance these individuals are 
homozygous dominant for 
brown coat color. As a result, 
in the third generation the 
recessive b allele is lost. 


Small populations are more susceptible to the forces of genetic drift. Large 
populations, on the other hand, are buffered against the effects of chance. If 
one individual of a population of 10 individuals happens to die at a young 
age before it leaves any offspring to the next generation, all of its genes— 
1/10 of the population’s gene pool—will be suddenly lost. In a population 
of 100, that’s only 1 percent of the overall gene pool; therefore, it is much 
less impactful on the population’s genetic structure. 


Genetic drift can also be magnified by natural events, such as a natural 
disaster that kills—at random—a large portion of the population. Known as 
the bottleneck effect, it results in a large portion of the genome suddenly 
being wiped out ({link]). In one fell swoop, the genetic structure of the 
survivors becomes the genetic structure of the entire population, which may 
be very different from the pre-disaster population. 


Original 
population 


Bottlenecking 
event 


Surviving 
population 


A chance event or catastrophe 
can reduce the genetic 
variability within a population. 


Another scenario in which populations might experience a strong influence 
of genetic drift is if some portion of the population leaves to start a new 
population in a new location or if a population gets divided by a physical 
barrier of some kind. In this situation, those individuals are unlikely to be 
representative of the entire population, which results in the founder effect. 
The founder effect occurs when the genetic structure changes to match that 
of the new population’s founding fathers and mothers. The founder effect is 
believed to have been a key factor in the genetic history of the Afrikaner 
population of Dutch settlers in South Africa, as evidenced by mutations that 
are common in Afrikaners but rare in most other populations. This is likely 
due to the fact that a higher-than-normal proportion of the founding 
colonists carried these mutations. As a result, the population expresses 
unusually high incidences of Huntington’s disease (HD) and Fanconi 
anemia (FA), a genetic disorder known to cause blood marrow and 
congenital abnormalities—even cancer, omote! 

A. J. Tipping et al., “Molecular and Genealogical Evidence for a Founder 
Effect in Fanconi Anemia Families of the Afrikaner Population of South 


Africa,” PNAS 98, no. 10 (2001): 5734-5739, doi: 
10.1073/pnas.091402398. 


Gene Flow 


Another important evolutionary force is gene flow: the flow of alleles in 
and out of a population due to the migration of individuals or gametes 
({link]). While some populations are fairly stable, others experience more 
flux. Many plants, for example, send their pollen far and wide, by wind or 
by bird, to pollinate other populations of the same species some distance 
away. Even a population that may initially appear to be stable, such as a 
pride of lions, can experience its fair share of immigration and emigration 
as developing males leave their mothers to seek out a new pride with 
genetically unrelated females. This variable flow of individuals in and out 
of the group not only changes the gene structure of the population, but it 
can also introduce new genetic variation to populations in different 
geological locations and habitats. 


ve. 
ae 


Gene flow can occur when an individual 
travels from one geographic location to 
another. 


Mutation 


Mutations are changes to an organism’s DNA and are an important driver of 
diversity in populations. Species evolve because of the accumulation of 
mutations that occur over time. The appearance of new mutations is the 
most common way to introduce novel genotypic and phenotypic variance. 
Some mutations are unfavorable or harmful and are quickly eliminated 
from the population by natural selection. Others are beneficial and will 
spread through the population. Whether or not a mutation is beneficial or 
harmful is determined by whether it helps an organism survive to sexual 
maturity and reproduce. Some mutations do not do anything and can linger, 
unaffected by natural selection, in the genome. Some can have a dramatic 
effect on a gene and the resulting phenotype. 


Nonrandom Mating 


If individuals nonrandomly mate with their peers, the result can be a 
changing population. There are many reasons nonrandom mating occurs. 
One reason is mate choice; for example, female peahens may prefer 
peacocks with bigger, brighter tails. Traits that lead to more matings for an 
individual become selected for by natural selection. One common form of 
mate choice, called assortative mating, is an individual’s preference to mate 
with partners who are phenotypically similar to themselves. 


Another cause of nonrandom mating is physical location. This is especially 
true in large populations spread over large geographic distances where not 
all individuals will have equal access to one another. Some might be miles 
apart through woods or over rough terrain, while others might live 
immediately nearby. 


Formation of New Species 


Introduction 

" As buds give rise by growth to fresh buds, and these, if vigorous, branch 
out and overtop on all sides many a feebler branch, so by generation I 
believe it has been with the great Tree of Life, which fills with its dead and 
broken branches the crust of the earth, and covers the surface with its ever 
branching and beautiful ramifications. " Charles Darwin, On the Origin of 
Species by Means of Natural Selection; or, The Preservation of Favoured 
Races in the Struggle for Life, 1859 


Darwin's insight about the branching tree of life is the easiest way to think 
about the origin of species. The twigs at the ends of branches may be 
different, but they all are connected and related. Although all life on earth 
shares various genetic similarities, only certain organisms combine genetic 
information by sexual reproduction and have offspring that can then 
successfully reproduce. Scientists call such organisms members of the same 
biological species. 


Species and the Ability to Reproduce 


A species is a group of individual organisms that interbreed and produce 
fertile, viable offspring. According to this definition, one species is 
distinguished from another when, in nature, it is not possible for matings 
between individuals from each species to produce fertile offspring. This 
idea of a species is called the biological species concept and is one of the 
most widely accepted species concepts. 


Members of the same species share both external and internal 
characteristics, which develop from their DNA. The closer relationship two 
organisms share, the more DNA they have in common, just like people and 
their families. Your DNA is likely to be more like your father or mother’s 
DNA than your cousin or grandparent’s DNA. Organisms of the same 
species have the highest level of DNA alignment and therefore share 
characteristics and behaviors that lead to successful reproduction. 


Species’ appearance can be misleading in suggesting an ability or inability 
to mate. For example, even though domestic dogs (Canis lupus familiaris) 
display phenotypic differences, such as size, build, and coat, most dogs can 
interbreed and produce viable puppies that can mature and sexually 
reproduce ([link]). 


The (a) poodle and (b) cocker spaniel can reproduce to 
produce a breed known as (c) the cockapoo. (credit a: 
modification of work by Sally Eller, Tom Reese; credit 
b: modification of work by Jeremy McWilliams; credit 
c: modification of work by Kathleen Conklin) 


In other cases, individuals may appear similar although they are not 
members of the same species. For example, even though bald eagles 
(Haliaeetus leucocephalus) and African fish eagles (Haliaeetus vocifer) are 
both birds and eagles, each belongs to a separate species group ([link]). If 
humans were to artificially intervene and fertilize the egg of a bald eagle 
with the sperm of an African fish eagle and a chick did hatch, that offspring, 
called a hybrid (a cross between two species), would probably be infertile 
—unable to successfully reproduce after it reached maturity. Different 
species may have different genes that are active in development; therefore, 
it may not be possible to develop a viable offspring with two different sets 
of directions. Thus, even though hybridization may take place, the two 
species still remain separate. 


The (a) African fish eagle is similar in 
appearance to the (b) bald eagle, but the two 
birds are members of different species. 
(credit a: modification of work by Nigel 
Wedge; credit b: modification of work by 
U.S. Fish and Wildlife Service) 


Populations of species share a gene pool: a collection of all the variants of 
genes in the species. Again, the basis to any changes in a group or 
population of organisms must be genetic for this is the only way to share 
and pass on traits. When variations occur within a species, they can only be 
passed to the next generation along two main pathways: asexual 
reproduction or sexual reproduction. The change will be passed on 
asexually simply if the reproducing cell possesses the changed trait. For the 
changed trait to be passed on by sexual reproduction, a gamete, such as a 
sperm or egg cell, must possess the changed trait. In other words, sexually- 
reproducing organisms can experience several genetic changes in their body 
cells, but if these changes do not occur in a sperm or egg cell, the changed 
trait will never reach the next generation. Only heritable traits can evolve. 
Therefore, reproduction plays a paramount role for genetic change to take 
root in a population or species. In short, organisms must be able to 
reproduce with each other to pass new traits to offspring. 


Speciation 


The biological definition of species, which works for sexually reproducing 
organisms, is a group of actually or potentially interbreeding individuals. 


There are exceptions to this rule. Many species are similar enough that 
hybrid offspring are possible and may often occur in nature, but for the 
majority of species this rule generally holds. In fact, the presence in nature 
of hybrids between similar species suggests that they may have descended 
from a single interbreeding species, and the speciation process may not yet 
be completed. 


Given the extraordinary diversity of life on the planet there must be 
mechanisms for speciation: the formation of two species from one original 
species. Darwin envisioned this process as a branching event and 
diagrammed the process in the only illustration found in On the Origin of 
Species ([{link]a). Compare this illustration to the diagram of elephant 
evolution ([link]b), which shows that as one species changes over time, it 
branches to form more than one new species, repeatedly, as long as the 
population survives or until the organism becomes extinct. 


Elephas 


) es : 2 Pipi lee <p pa ee ESS =f2p, Loxodonta 
Se ‘a aoe Gn: =“ ania 7+ ™Y | (asian elephant) [ 


_,, (African elephant) 


Mammuthus 
(mammoth) 


Mammut Stegodon 
(mastodon) 


(a) (b) 


The only illustration in Darwin's On the Origin of Species is (a) a 
diagram showing speciation events leading to biological diversity. The 
diagram shows similarities to phylogenetic charts that are drawn today 
to illustrate the relationships of species. (b) Modern elephants evolved 
from the Palaeomastodon, a species that lived in Egypt 35-50 million 

years ago. 


For speciation to occur, two new populations must be formed from one 
original population and they must evolve in such a way that it becomes 
impossible for individuals from the two new populations to interbreed. 
Biologists have proposed mechanisms by which this could occur that fall 
into two broad categories. Allopatric speciation (allo- = "other"; -patric = 
"homeland") involves geographic separation of populations from a parent 
species and subsequent evolution. Sympatric speciation (sym- = "same"; - 
patric = "homeland") involves speciation occurring within a parent species 
remaining in one location. 


Biologists think of speciation events as the splitting of one ancestral species 
into two descendant species. There is no reason why there might not be 
more than two species formed at one time except that it is less likely and 
multiple events can be conceptualized as single splits occurring close in 
time. 


Allopatric Speciation 


A geographically continuous population has a gene pool that is relatively 
homogeneous. Gene flow, the movement of alleles across the range of the 
species, is relatively free because individuals can move and then mate with 
individuals in their new location. Thus, the frequency of an allele at one end 
of a distribution will be similar to the frequency of the allele at the other 
end. When populations become geographically discontinuous, that free- 
flow of alleles is prevented. When that separation lasts for a period of time, 
the two populations are able to evolve along different trajectories. Thus, 
their allele frequencies at numerous genetic loci gradually become more 
and more different as new alleles independently arise by mutation in each 
population. Typically, environmental conditions, such as climate, resources, 
predators, and competitors for the two populations will differ causing 
natural selection to favor divergent adaptations in each group. 


Isolation of populations leading to allopatric speciation can occur in a 
variety of ways: a river forming a new branch, erosion forming a new 
valley, a group of organisms traveling to a new location without the ability 


to return, or seeds floating over the ocean to an island. The nature of the 
geographic separation necessary to isolate populations depends entirely on 
the biology of the organism and its potential for dispersal. If two flying 
insect populations took up residence in separate nearby valleys, chances 
are, individuals from each population would fly back and forth continuing 
gene flow. However, if two rodent populations became divided by the 
formation of a new lake, continued gene flow would be unlikely; therefore, 
speciation would be more likely. 


Biologists group allopatric processes into two categories: dispersal and 
vicariance. Dispersal is when a few members of a species move to a new 
geographical area, and vicariance is when a natural situation arises to 
physically divide organisms. 


Scientists have documented numerous cases of allopatric speciation taking 
place. For example, along the west coast of the United States, two separate 
sub-species of spotted owls exist. The northern spotted owl has genetic and 
phenotypic differences from its close relative: the Mexican spotted owl, 
which lives in the south ([Link]). 


Mexican Spotted Owl 


The northern spotted owl and 
the Mexican spotted owl 
inhabit geographically 
separate locations with 
different climates and 
ecosystems. The owl is an 
example of allopatric 
speciation. (credit "northern 
spotted owl": modification of 
work by John and Karen 
Hollingsworth; credit 
"Mexican spotted owl": 
modification of work by Bill 
Radke) 


Additionally, scientists have found that the further the distance between two 
groups that once were the same species, the more likely it is that speciation 
will occur. This seems logical because as the distance increases, the various 
environmental factors would likely have less in common than locations in 
close proximity. Consider the two owls: in the north, the climate is cooler 
than in the south; the types of organisms in each ecosystem differ, as do 
their behaviors and habits; also, the hunting habits and prey choices of the 
southern owls vary from the northern owls. These variances can lead to 
evolved differences in the owls, and speciation likely will occur. 


Adaptive Radiation 


In some cases, a population of one species disperses throughout an area, 
and each finds a distinct niche or isolated habitat. Over time, the varied 
demands of their new lifestyles lead to multiple speciation events 
originating from a single species. This is called adaptive radiation because 
many adaptations evolve from a single point of origin; thus, causing the 
species to radiate into several new ones. Island archipelagos like the 
Hawaiian Islands provide an ideal context for adaptive radiation events 


because water surrounds each island which leads to geographical isolation 
for many organisms. The Hawaiian honeycreeper illustrates one example of 
adaptive radiation. From a single species, called the founder species, 
numerous species have evolved, including the six shown in [link]. 


The honeycreeper birds illustrate adaptive 
radiation. From one original species of 
bird, multiple others evolved, each with 

its own distinctive characteristics. 


Notice the differences in the species’ beaks in [link]. Evolution in response 
to natural selection based on specific food sources in each new habitat led 
to evolution of a different beak suited to the specific food source. The seed- 
eating bird has a thicker, stronger beak which is suited to break hard nuts. 
The nectar-eating birds have long beaks to dip into flowers to reach the 
nectar. The insect-eating birds have beaks like swords, appropriate for 


stabbing and impaling insects. Darwin’s finches are another example of 
adaptive radiation in an archipelago. 


Sympatric Speciation 


Can divergence occur if no physical barriers are in place to separate 
individuals who continue to live and reproduce in the same habitat? The 
answer is yes. The process of speciation within the same space is called 
sympatric speciation; the prefix “sym” means same, so “sympatric” means 
“same homeland” in contrast to “allopatric” meaning “other homeland.” A 
number of mechanisms for sympatric speciation have been proposed and 
studied. 


One form of sympatric speciation can begin with a serious chromosomal 
error during cell division. In a normal cell division event chromosomes 
replicate, pair up, and then separate so that each new cell has the same 
number of chromosomes. However, sometimes the pairs separate and the 
end cell product has too many or too few individual chromosomes in a 
condition called aneuploidy ([link]). 


Note: 
Aneuploidy Resulting in Offspring with 2n + 1 or 2n - 1 Chromosomes 
Nondisjunction Mating with 
during meiosis normal gamete 


2n 


eo -& 
= 
Oo e+ 


Diploid (2n) 


Aneuploidy results when the gametes have too 
many or too few chromosomes due to 
nondisjunction during meiosis. In the example 
shown here, the resulting offspring will have 
2n+1 or 2n-1 chromosomes 


Polyploidy is a condition in which a cell or organism has an extra set, or 
sets, of chromosomes. Scientists have identified two main types of 
polyploidy that can lead to reproductive isolation of an individual in the 
polyploidy state. Reproductive isolation is the inability to interbreed. In 
some cases, a polyploid individual will have two or more complete sets of 
chromosomes from its own species in a condition called autopolyploidy 
({link]). The prefix “auto-” means “self,” so the term means multiple 
chromosomes from one’s own species. Polyploidy results from an error in 
meiosis in which all of the chromosomes move into one cell instead of 
separating. 


of Chromosomes 


— 


Diploid parent (2n) Polyploid offspring (4n) 


Autopolyploidy Resulting in Offspring with Two Sets 


Autopolyploidy results when 
mitosis is not followed by 
cytokinesis. 


For example, if a plant species with 2n = 6 produces autopolyploid gametes 
that are also diploid (2n = 6, when they should be n = 3), the gametes now 
have twice as many chromosomes as they should have. These new gametes 
will be incompatible with the normal gametes produced by this plant 
species. However, they could either self-pollinate or reproduce with other 
autopolyploid plants with gametes having the same diploid number. In this 
way, sympatric speciation can occur quickly by forming offspring with 4n 
called a tetraploid. These individuals would immediately be able to 
reproduce only with those of this new kind and not those of the ancestral 
species. 


The other form of polyploidy occurs when individuals of two different 
species reproduce to form a viable offspring called an allopolyploid. The 
prefix “allo-” means “other” (recall from allopatric): therefore, an 
allopolyploid occurs when gametes from two different species combine. 
[link] illustrates one possible way an allopolyploid can form. Notice how it 
takes two generations, or two reproductive acts, before the viable fertile 
hybrid results. 


Alloploidy Resulting from Viable Matings between Two Species 


Normal gamete 


Oy 4 Polyploid 
First gamete Second 
Species 1 mating mating 
4s 
/ \he 


Species 2 Polyploid gamete Normal gamete 


Alloploidy results when two species mate to 
produce viable offspring. In the example shown, a 
normal gamete from one species fuses with a 
polyploidy gamete from another. Two matings are 
necessary to produce viable offspring. 


The cultivated forms of wheat, cotton, and tobacco plants are all 
allopolyploids. Although polyploidy occurs occasionally in animals, it takes 
place most commonly in plants. (Animals with any of the types of 
chromosomal aberrations described here are unlikely to survive and 
produce normal offspring.) Scientists have discovered more than half of all 
plant species studied relate back to a species evolved through polyploidy. 
With such a high rate of polyploidy in plants, some scientists hypothesize 
that this mechanism takes place more as an adaptation than as an error. 


Reproductive Isolation 


Given enough time, the genetic and phenotypic divergence between 
populations will affect characters that influence reproduction: if individuals 
of the two populations were to be brought together, mating would be less 
likely, but if mating occurred, offspring would be non-viable or infertile. 
Many types of diverging characters may affect the reproductive isolation, 
the ability to interbreed, of the two populations. 


Reproductive isolation can take place in a variety of ways. Scientists 
organize them into two groups: prezygotic barriers and postzygotic barriers. 
Recall that a zygote is a fertilized egg: the first cell of the development of 
an organism that reproduces sexually. Therefore, a prezygotic barrier is a 
mechanism that blocks reproduction or prevents fertilization when 
organisms attempt reproduction. A postzygotic barrier occurs after 
fertilization; this includes organisms that don’t survive the embryonic stage 
and those that are born sterile. 


Some types of prezygotic barriers prevent reproduction entirely. Many 
organisms only reproduce at certain times of the year, often just annually. 
Differences in breeding schedules, called temporal isolation, can act as a 
form of reproductive isolation. For example, two species of frogs inhabit 
the same area, but one reproduces from January to March, whereas the 
other reproduces from March to May ((link]). 


(a) (b) 


These two related frog species exhibit temporal 
reproductive isolation. (a) Rana aurora breeds 
earlier in the year than (b) Rana boylii. (credit 
a: modification of work by Mark R. Jennings, 

USFWS; credit b: modification of work by 
Alessandro Catenazzi) 


In some cases, populations of a species move or are moved to a new habitat 
and take up residence in a place that no longer overlaps with the other 
populations of the same species. This situation is called habitat isolation. 
Reproduction with the parent species ceases, and a new group exists that is 
now reproductively and genetically independent. For example, a cricket 
population that was divided after a flood could no longer interact with each 
other. Over time, the forces of natural selection, mutation, and genetic drift 
will likely result in the divergence of the two groups ([link]). 


(a) Gryllus pennsylvanicus prefers (b) Gryllus firmus prefers loamy soil. 
sandy soil. 


Speciation can occur when two populations 
occupy different habitats. The habitats need 
not be far apart. The cricket (a) Gryllus 
pennsylvanicus prefers sandy soil, and the 
cricket (b) Gryllus firmus prefers loamy soil. 
The two species can live in close proximity, 
but because of their different soil 
preferences, they became genetically 
isolated. 


Behavioral isolation occurs when the presence or absence of a specific 
behavior prevents reproduction from taking place. For example, male 
fireflies use specific light patterns to attract females. Various species of 
fireflies display their lights differently. If a male of one species tried to 
attract the female of another, she would not recognize the light pattern and 
would not mate with the male. 


Other prezygotic barriers work when differences in their gamete cells (eggs 
and sperm) prevent fertilization from taking place; this is called a gametic 
barrier. Similarly, in some cases closely related organisms try to mate, but 
their reproductive structures simply do not fit together. For example, 
damselfly males of different species have differently shaped reproductive 
organs. If one species tries to mate with the female of another, their body 
parts simply do not fit together. ((link]). 


GS & ame 


The shape of the male reproductive organ varies 
among male damselfly species, and is only compatible 
with the female of that species. Reproductive organ 


incompatibility keeps the species reproductively 
isolated. 


In plants, certain structures aimed to attract one type of pollinator 
simultaneously prevent a different pollinator from accessing the pollen. The 
tunnel through which an animal must access nectar can vary widely in 
length and diameter, which prevents the plant from being cross-pollinated 
with a different species ((link]). 


(a) Honeybee drinking nectar (b) Ruby-throated hummingbird drinking nectar from a 
from a foxglove flower trumpet creeper flower 


Some flowers have evolved to attract certain 
pollinators. The (a) wide foxglove flower is 
adapted for pollination by bees, while the (b) 
long, tube-shaped trumpet creeper flower is 
adapted for pollination by humming birds. 


When fertilization takes place and a zygote forms, postzygotic barriers can 
prevent reproduction. Hybrid individuals in many cases cannot form 
normally in the womb and simply do not survive past the embryonic stages. 
This is called hybrid inviability because the hybrid organisms simply are 
not viable. In another postzygotic situation, reproduction leads to the birth 
and growth of a hybrid that is sterile and unable to reproduce offspring of 
their own; this is called hybrid sterility. 


Habitat Influence on Speciation 


Sympatric speciation may also take place in ways other than polyploidy. 
For example, consider a species of fish that lives in a lake. As the 
population grows, competition for food also grows. Under pressure to find 
food, suppose that a group of these fish had the genetic flexibility to 
discover and feed off another resource that was unused by the other fish. 
What if this new food source was found at a different depth of the lake? 
Over time, those feeding on the second food source would interact more 
with each other than the other fish; therefore, they would breed together as 
well. Offspring of these fish would likely behave as their parents: feeding 
and living in the same area and keeping separate from the original 
population. If this group of fish continued to remain separate from the first 
population, eventually sympatric speciation might occur as more genetic 
differences accumulated between them. 


This scenario does play out in nature, as do others that lead to reproductive 
isolation. One such place is Lake Victoria in Africa, famous for its 
sympatric speciation of cichlid fish. Researchers have found hundreds of 
sympatric speciation events in these fish, which have not only happened in 
great number, but also over a short period of time. [link] shows this type of 
speciation among a cichlid fish population in Nicaragua. In this locale, two 
types of cichlids live in the same geographic location but have come to have 
different morphologies that allow them to eat various food sources. 


ABS 


Thin-lipped cichlid Thick-lipped cichlid 


Cichlid fish from Lake Apoyeque, Nicaragua, show evidence 
of sympatric speciation. Lake Apoyeque, a crater lake, is 1800 
years old, but genetic evidence indicates that the lake was 
populated only 100 years ago by a single population of cichlid 


fish. Nevertheless, two populations with distinct morphologies 
and diets now exist in the lake, and scientists believe these 
populations may be in an early stage of speciation. 


Energy and Metabolism 


Introduction 

" [In research on bacteria metabolism] we have indeed much the same 
position as an observer trying to gain an idea of the life of a household by 
careful scrutiny of the persons and material arriving or leaving the house; 
we keep accurate records of the foods and commodities left at the door and 
patiently examine the contents of the dust-bin and endeavour to deduce 
from such data the events occurring within the closed doors. " Marjory 
Stephenson (1930) 


Metabolism is indeed most closely studied by marking what goes in and 
what comes out, both in terms of materials and energy. Scientists use the 
term bioenergetics to discuss the concept of energy flow ([link]) through 
living systems from ecosystems to cells. Cellular processes such as the 
building and breaking down of complex molecules occur through stepwise 
chemical reactions. Some of these chemical reactions are spontaneous and 
release energy, whereas others require energy to proceed. Just as living 
things must continually consume food to replenish what has been used, 
cells must continually produce more energy to replenish that used by the 
many energy-requiring chemical reactions that constantly take place. All of 
the chemical reactions that take place inside cells, including those that use 
energy and those that release energy, are the cell’s metabolism. 


% 


Most life forms on earth get their energy from the sun. Various 
metabolic processes harvest and harness this energy which ultimately 
leaves the system as heat (24 Law of Thermodynamics). The dashed 


lines represent energy and the solid lines represent nutrients. (Image by 
Eva Horne and Robert Bear) 


Metabolism of Carbohydrates 


The metabolism of sugar (a simple carbohydrate) is a classic example of the 
many cellular processes that use and produce energy. Living things 
consume sugar as a major energy source, because sugar molecules have a 
great deal of energy stored within their bonds. The breakdown of glucose, a 
simple sugar, is described by the equation: 

Equation: 


CgH20¢ “re 605 — 6CO, ae 6H,O + energy 


Carbohydrates that are consumed have their origins in photosynthesizing 
organisms like plants ((link]). During photosynthesis, plants use the energy 
of sunlight to convert carbon dioxide gas (CO>) into sugar molecules, like 
glucose (CgH,20¢). Because this process involves synthesizing a larger, 
energy-storing molecule, it requires an input of energy to proceed. The 
synthesis of glucose is described by this equation (notice that it is the 
reverse of the previous equation): 

Equation: 


6CO, a 6H,O + energy —> CgH20¢ a 60, 


During the chemical reactions of photosynthesis, energy is provided in the 
form of a very high-energy molecule called ATP, or adenosine triphosphate, 
which is the primary energy currency of all cells. Just as the dollar is used 
as Currency to buy goods, cells use molecules of ATP as energy currency to 
perform immediate work. The sugar (glucose) is stored as starch or 
glycogen. Energy-storing polymers like these are broken down into glucose 
to supply molecules of ATP. 


Solar energy is required to synthesize a molecule of glucose during the 
reactions of photosynthesis. In photosynthesis, light energy from the sun is 
initially transformed into chemical energy that is temporally stored in the 
energy carrier molecules ATP and NADPH (nicotinamide adenine 
dinucleotide phosphate). The stored energy in ATP and NADPH is then 
used later in photosynthesis to build one molecule of glucose from six 
molecules of CO». This process is analogous to eating breakfast in the 
morning to acquire energy for your body that can be used later in the day. 
Under ideal conditions, energy from 18 molecules of ATP is required to 
synthesize one molecule of glucose during the reactions of photosynthesis. 
Glucose molecules can also be combined with and converted into other 
types of sugars. When sugars are consumed, molecules of glucose 
eventually make their way into each living cell of the organism. Inside the 
cell, each sugar molecule is broken down through a complex series of 
chemical reactions. The goal of these reactions is to harvest the energy 
stored inside the sugar molecules. The harvested energy is used to make 
high-energy ATP molecules, which can be used to perform work, powering 
many chemical reactions in the cell. The amount of energy needed to make 
one molecule of glucose from six molecules of carbon dioxide is 18 
molecules of ATP and 12 molecules of NADPH (each one of which is 
energetically equivalent to three molecules of ATP), or a total of 54 
molecule equivalents required for the synthesis of one molecule of glucose. 
This process is a fundamental and efficient way for cells to generate the 
molecular energy that they require. 


Plants, like this oak tree and acorn, use energy from 
sunlight to make sugar and other organic molecules. 
Both plants and animals (like this squirrel) use cellular 
respiration to derive energy from the organic molecules 
originally produced by plants. (credit “acorn”: 
modification of work by Noel Reynolds; credit 
“squirrel”: modification of work by Dawn Huczek) 


Metabolic Pathways 


The processes of making and breaking down sugar molecules illustrate two 
types of metabolic pathways. A metabolic pathway is a series of 
interconnected biochemical reactions that convert a substrate molecule or 
molecules, step-by-step, through a series of metabolic intermediates, 
eventually yielding a final product or products. In the case of sugar 
metabolism, the first metabolic pathway synthesized sugar from smaller 
molecules, and the other pathway broke sugar down into smaller molecules. 
These two opposite processes—the first requiring energy and the second 
producing energy—are referred to as anabolic (building) and catabolic 
(breaking down) pathways, respectively. Consequently, metabolism is 
composed of building (anabolism) and degradation (catabolism). 


Note: 
Evolution Connection 


This tree shows the evolution of the various branches of 

life. The vertical dimension is time. Early life forms, in 

blue, used anaerobic metabolism to obtain energy from 
their surroundings. 


Evolution of Metabolic Pathways 

There is more to the complexity of metabolism than understanding the 
metabolic pathways alone. Metabolic complexity varies from organism to 
organism. Photosynthesis is the primary pathway in which photosynthetic 
organisms like plants (the majority of global synthesis is done by 
planktonic algae) harvest the sun’s energy and convert it into 
carbohydrates. The by-product of photosynthesis is oxygen, required by 
some cells to carry out cellular respiration. During cellular respiration, 
oxygen aids in the catabolic breakdown of carbon compounds, like 
carbohydrates. Among the products of this catabolism are CO, and ATP. In 
addition, some eukaryotes perform catabolic processes without oxygen 
(fermentation); that is, they perform or use anaerobic metabolism. 
Organisms probably evolved anaerobic metabolism to survive (living 
organisms came into existence about 3.8 billion years ago, when the 
atmosphere lacked oxygen). Despite the differences between organisms 
and the complexity of metabolism, researchers have found that all branches 
of life share some of the same metabolic pathways, suggesting that all 


organisms evolved from the same ancient common ancestor ({link]). 
Evidence indicates that over time, the pathways diverged, adding 
specialized enzymes to allow organisms to better adapt to their 
environment, thus increasing their chance to survive. However, the 
underlying principle remains that all organisms must harvest energy from 
their environment and convert it to ATP to carry out cellular functions. 


Anabolic and Catabolic Pathways 


Anabolic pathways require an input of energy to synthesize complex 
molecules from simpler ones. Synthesizing sugar from CO, is one example. 
Other examples are the synthesis of large proteins from amino acid building 
blocks, and the synthesis of new DNA strands from nucleic acid building 
blocks. These biosynthetic processes are critical to the life of the cell, take 
place constantly, and demand energy provided by ATP and other high- 
energy molecules like NADH (nicotinamide adenine dinucleotide) and 
NADPH ([link]). 


ATP is an important molecule for cells to have in sufficient supply at all 
times. The breakdown of sugars illustrates how a single molecule of 
glucose can store enough energy to make a great deal of ATP, 36 to 38 
molecules. This is a catabolic pathway. Catabolic pathways involve the 
degradation (or breakdown) of complex molecules into simpler ones. 
Molecular energy stored in the bonds of complex molecules is released in 
catabolic pathways and harvested in such a way that it can be used to 
produce ATP. Other energy-storing molecules, such as fats, are also broken 
down through similar catabolic reactions to release energy and make ATP 


(Link]). 


It is important to know that the chemical reactions of metabolic pathways 
don’t take place spontaneously. Each reaction step is facilitated, or 
catalyzed, by a protein called an enzyme. Enzymes are important for 
catalyzing all types of biological reactions—those that require energy as 
well as those that release energy. 


Metabolic pathways 


Anabolic: Small molecules are assembled into large ones. Energy is required. 


C) C) @ OC) +Energyle ees 


Catabolic: Large molecules are broken down into small ones. Energy is released. 


©0800 — © © © O +=» 


Anabolic pathways are those that require energy to 
synthesize larger molecules. Catabolic pathways 
are those that generate energy by breaking down 

larger molecules. Both types of pathways are 
required for maintaining the cell’s energy balance. 


Thermodynamics 


Introduction 

" A theory is the more impressive the greater the simplicity of its premises 
is, the more different kinds of things it relates, and the more extended is its 
area of applicability. Therefore the deep impression which classical 
thermodynamics made upon me. It is the only physical theory of universal 
content concerning which I am convinced that within the framework of the 
applicability of its basic concepts, it will never be overthrown. " Albert 
Einstein (1946) 


That high praise from Einstein still rings true today; the laws of 
thermodynamics can still explain many interactions, both in the biotic and 
abiotic realms. Thermodynamics refers to the study of energy and energy 
transfer involving physical matter. The matter and its environment relevant 
to a particular case of energy transfer are classified as a system, and 
everything outside of that system is called the surroundings. For instance, 
when heating a pot of water on the stove, the system includes the stove, the 
pot, and the water. Energy is transferred within the system (between the 
stove, pot, and water). There are two types of systems: open and closed. An 
open system is one in which energy can be transferred between the system 
and its surroundings. The stovetop system is open because heat can be lost 
into the air. A closed system is one that cannot transfer energy to its 
surroundings. 


Biological organisms are open systems. Energy is exchanged between them 
and their surroundings, as they consume energy-storing molecules and 
release energy to the environment by doing work. Like all things in the 
physical world, energy is subject to the laws of physics. The laws of 
thermodynamics govern the transfer of energy in and among all systems in 
the universe. 


The First Law of Thermodynamics 


The first law of thermodynamics deals with the total amount of energy in 
the universe. It states that this total amount of energy in the universe is 
constant. In other words, there has always been, and always will be, exactly 


the same amount of energy in the universe. Energy exists in many different 
forms. According to the first law of thermodynamics, energy may be 
transferred from place to place or transformed into different forms, but it 
cannot be created or destroyed. The transfers and transformations of energy 
take place around us all the time. Light bulbs transform electrical energy 
into light energy. Gas stoves transform chemical energy from natural gas 
into heat energy. Plants perform one of the most biologically useful energy 
transformations on earth: that of converting the energy of sunlight into the 
chemical energy stored within organic molecules. Some examples of energy 
transformations are shown in [link]. 


The challenge for all living organisms is to obtain energy from their 
surroundings in forms that they can transfer or transform into usable energy 
to do work. Living cells have evolved to meet this challenge very well. 
Chemical energy stored within organic molecules such as sugars and fats is 
transformed through a series of cellular chemical reactions into energy 
within molecules of ATP. Energy in ATP molecules is easily accessible to 
do work. Examples of the types of work that cells need to do include 
building complex molecules, transporting materials, powering the beating 
motion of cilia or flagella, contracting muscle fibers to create movement, 
and reproduction. 


Chemical energy Light energy 


>» > 


Kinetic energy Chemical energy 


Shown are two examples of 
energy being transferred from 
one system to another and 
transformed from one form to 
another. Humans can convert 
the chemical energy in food, 
like this ice cream cone, into 
kinetic energy (the energy of 
movement to ride a bicycle). 
Plants can convert 
electromagnetic radiation (light 
energy) from the sun into 
chemical energy. (credit “ice 
cream”: modification of work 
by D. Sharon Pruitt; credit “kids 
on bikes”: modification of work 
by Michelle Riggen-Ransom; 


credit “leaf”: modification of 
work by Cory Zanker) 


The Second Law of Thermodynamics 


A living cell’s primary tasks of obtaining, transforming, and using energy to 
do work may seem simple. However, the second law of thermodynamics 
explains why these tasks are harder than they appear. None of the energy 
transfers we’ve discussed, along with all energy transfers and 
transformations in the universe, is completely efficient. In every energy 
transfer, some amount of energy is lost in a form that is unusable. In most 
cases, this form is heat energy. Thermodynamically, heat energy is defined 
as the energy transferred from one system to another that is not doing work. 
For example, when an airplane flies through the air, some of the energy of 
the flying plane is lost as heat energy due to friction with the surrounding 
air. This friction actually heats the air by temporarily increasing the speed 
of air molecules. Likewise, some energy is lost as heat energy during 
cellular metabolic reactions. This is good for warm-blooded creatures like 
us, because heat energy helps to maintain our body temperature. Strictly 
speaking, no energy transfer is completely efficient, because some energy is 
lost in an unusable form. 


An important concept in physical systems is that of order and disorder (also 
known as randomness). The more energy that is lost by a system to its 
surroundings, the less ordered and more random the system is. Scientists 
refer to the measure of randomness or disorder within a system as entropy. 
High entropy means high disorder and low energy ([link]). To better 
understand entropy, think of a student’s bedroom. If no energy or work were 
put into it, the room would quickly become messy. It would exist in a very 
disordered state, one of high entropy. Energy must be put into the system, in 
the form of the student doing work and putting everything away, in order to 
bring the room back to a state of cleanliness and order. This state is one of 
low entropy. Similarly, a car or house must be constantly maintained with 
work in order to keep it in an ordered state. Left alone, the entropy of the 
house or car gradually increases through rust and degradation. Molecules 
and chemical reactions have varying amounts of entropy as well. For 


example, as chemical reactions reach a state of equilibrium, entropy 
increases, and as molecules at a high concentration in one place diffuse and 
spread out, entropy also increases. 


Note: 

Scientific Connection 

Transfer of Energy and the Resulting Entropy 

Set up a simple experiment to understand how energy is transferred and 
how a change in entropy results. 


1. Take a block of ice. This is water in solid form, so it has a high 
structural order. This means that the molecules cannot move very 
much and are in a fixed position. The temperature of the ice is 0°C. 
As aresult, the entropy of the system is low. 

2. Allow the ice to melt at room temperature. What is the state of 
molecules in the liquid water now? How did the energy transfer take 
place? Is the entropy of the system higher or lower? Why? 

3. Heat the water to its boiling point. What happens to the entropy of the 
system when the water is heated? 


All physical systems can be thought of in this way: Living things are highly 
ordered, requiring constant energy input to be maintained in a state of low 
entropy. As living systems take in energy-storing molecules and transform 
them through chemical reactions, they lose some amount of usable energy 
in the process, because no reaction is completely efficient. They also 
produce waste and by-products that aren’t useful energy sources. This 
process increases the entropy of the system’s surroundings. Since all energy 
transfers result in the loss of some usable energy, the second law of 
thermodynamics states that every energy transfer or transformation 
increases the entropy of the universe. Even though living things are highly 
ordered and maintain a state of low entropy, the entropy of the universe in 
total is constantly increasing due to the loss of usable energy with each 


energy transfer that occurs. Essentially, living things are in a continuous 
uphill battle against this constant increase in universal entropy. 


Increasing 
entropy 


Entropy is a measure of 
randomness or disorder in a 
system. Gases have higher 
entropy than liquids, and liquids 
have higher entropy than solids. 


Potential, Kinetic, and Free Energy 


Introduction 

"Energie is the operation, efflux or activity of any being: as the light of the 
Sunne is the energie of the Sunne, and every phantasm of the soul is the 
energie of the soul. " Henry More (1642), this is the first recorded definition 
of the term energy in English. 


Energy is defined as the ability to do work. As you know, energy exists in 
different forms. For example, chemical energy, electrical energy, light 
energy, and heat energy are all different types of energy. While these are all 
familiar types of energy that one can see or feel, there is another type of 
energy that is much less tangible. This energy is associated with something 
as simple as an object held above the ground. In order to appreciate the way 
energy flows into and out of biological systems, it is important to 
understand more about the different types of energy that exist in the 
physical world. 


Types of Energy 


When an object is in motion, there is energy associated with that object. In 
the example of an airplane in flight, there is a great deal of energy 
associated with the motion of the airplane. This is because moving objects 
are capable of enacting a change, or doing work. Think of a wrecking ball. 
Even a slow-moving wrecking ball can do a great deal of damage to other 
objects. However, a wrecking ball that is not in motion is incapable of 
performing work. Energy associated with objects in motion is called kinetic 
energy. A speeding bullet, a walking person, the rapid movement of 
molecules in the air (which produces heat), and electromagnetic radiation 
like light all have kinetic energy. 


Now what if that same motionless wrecking ball is lifted two stories above 
a car with a crane? If the suspended wrecking ball is unmoving, is there 
energy associated with it? The answer is yes. The suspended wrecking ball 
has energy associated with it that is fundamentally different from the kinetic 
energy of objects in motion. This form of energy results from the fact that 
there is the potential for the wrecking ball to do work. If it is released, 


indeed it would do work. Because this type of energy refers to the potential 
to do work, it is called potential energy. Objects transfer their energy 
between kinetic and potential in the following way: As the wrecking ball 
hangs motionless, it has 0 kinetic and 100 percent potential energy. Once it 
is released, its kinetic energy begins to increase because it builds speed due 
to gravity. At the same time, as it nears the ground, it loses potential energy. 
Somewhere mid-fall it has 50 percent kinetic and 50 percent potential 
energy. Just before it hits the ground, the ball has nearly lost its potential 
energy and has near-maximal kinetic energy. Other examples of potential 
energy include the energy of water held behind a dam ([link]), or a person 
about to skydive out of an airplane. 


Water behind a dam has potential energy. Moving water, 
such as in a waterfall or a rapidly flowing river, has 
kinetic energy. (credit “dam”: modification of work by 
"Pascal"/Flickr; credit “waterfall”: modification of work 
by Frank Gualtieri) 


Potential energy is not only associated with the location of matter (such as a 
child sitting on a tree branch), but also with the structure of matter. A spring 
on the ground has potential energy if it is compressed; so does a rubber 
band that is pulled taut. The very existence of living cells relies heavily on 
structural potential energy. On a chemical level, the bonds that hold the 


atoms of molecules together have potential energy. Remember that anabolic 
cellular pathways require energy to synthesize complex molecules from 
simpler ones, and catabolic pathways release energy when complex 
molecules are broken down. The fact that energy can be released by the 
breakdown of certain chemical bonds implies that those bonds have 
potential energy. In fact, there is potential energy stored within the bonds of 
all the food molecules we eat, which is eventually harnessed for use. This is 
because these bonds can release energy when broken. The type of potential 
energy that exists within chemical bonds, and is released when those bonds 
are broken, is called chemical energy ([link]). Chemical energy is 
responsible for providing living cells with energy from food. The release of 
energy is brought about by breaking the molecular bonds within fuel 
molecules. 


The molecules in gasoline (octane, 
the chemical formula shown) 
contain chemical energy within 
the chemical bonds. This energy is 


transformed into kinetic energy 
that allows a car to race on a 
racetrack. (credit “car”: 
modification of work by Russell 
Trow) 


Free Energy 


After learning that chemical reactions release energy when energy-storing 
bonds are broken, an important next question is how is the energy 
associated with chemical reactions quantified and expressed? How can the 
energy released from one reaction be compared to that of another reaction? 
A measurement of free energy is used to quantitate these energy transfers. 
Free energy is called Gibbs free energy (abbreviated with the letter G) after 
Josiah Willard Gibbs, the scientist who developed the measurement. Recall 
that according to the second law of thermodynamics, all energy transfers 
involve the loss of some amount of energy in an unusable form such as 
heat, resulting in entropy. Gibbs free energy specifically refers to the energy 
associated with a chemical reaction that is available after entropy is 
accounted for. In other words, Gibbs free energy is usable energy, or energy 
that is available to do work. So, every chemical reaction involves a change 
in free energy, called delta G (AG). 


Endergonic Reactions and Exergonic Reactions 


If energy is released during a chemical reaction, then the resulting value 
from the above equation will be a negative number. In other words, 
reactions that release energy have a AG < 0. A negative AG also means that 
the products of the reaction have less free energy than the reactants, because 
they gave off some free energy during the reaction. Reactions that have a 
negative AG and consequently release free energy are called exergonic 
reactions. Think: exergonic means energy is exiting the system. These 
reactions are also referred to as spontaneous reactions, because they can 


occur without the addition of energy into the system. Understanding which 
chemical reactions are spontaneous and release free energy is extremely 
useful for biologists, because these reactions can be harnessed to perform 
work inside the cell. An important distinction must be drawn between the 
term spontaneous and the idea of a chemical reaction that occurs 
immediately. Contrary to the everyday use of the term, a spontaneous 
reaction is not one that suddenly or quickly occurs. The rusting of iron is an 
example of a spontaneous reaction that occurs slowly, little by little, over 
time. 


If a chemical reaction requires an input of energy rather than releasing 
energy, then the AG for that reaction will be a positive value. In this case, 
the products have more free energy than the reactants. Thus, the products of 
these reactions can be thought of as energy-storing molecules. These 
chemical reactions are called endergonic reactions, and they are non- 
spontaneous. An endergonic reaction will not take place on its own without 
the addition of free energy. 


Let’s revisit the example of the synthesis and breakdown of the food 
molecule, glucose. Remember that the building of complex molecules, such 
as sugars, from simpler ones is an anabolic process and requires energy. 
Therefore, the chemical reactions involved in anabolic processes are 
endergonic reactions. On the other hand, the catabolic process of breaking 
sugar down into simpler molecules releases energy in a series of exergonic 
reactions. Like the example of rust above, the breakdown of sugar involves 
spontaneous reactions, but these reactions don’t occur instantaneously. 
[link] shows some other examples of endergonic and exergonic reactions. 
Later sections will provide more information about what else is required to 
make even spontaneous reactions happen more efficiently. 


(c) 


Shown are some examples of endergonic 
processes (ones that require energy) and 
exergonic processes (ones that release 
energy). These include (a) a compost pile 
decomposing, (b) a chick hatching from a 
fertilized egg, (c) sand art being destroyed, 
and (d) a ball rolling down a hill. (credit a: 
modification of work by Natalie Maynor; 
credit b: modification of work by USDA; 
credit c: modification of work by 
“Athlex”/Flickr; credit d: modification of 
work by Harry Malsch) 


An important concept in the study of metabolism and energy is that of 
chemical equilibrium. Most chemical reactions are reversible. They can 
proceed in both directions, releasing energy into their environment in one 
direction, and absorbing it from the environment in the other direction 
({link]). The same is true for the chemical reactions involved in cell 
metabolism, such as the breaking down and building up of proteins into and 
from individual amino acids, respectively. Reactants within a closed system 


will undergo chemical reactions in both directions until a state of 
equilibrium is reached. This state of equilibrium is one of the lowest 
possible free energy and a state of maximal entropy. Energy must be put 
into the system to push the reactants and products away from a state of 
equilibrium. Either reactants or products must be added, removed, or 
changed. If a cell were a closed system, its chemical reactions would reach 
equilibrium, and it would die because there would be insufficient free 
energy left to perform the work needed to maintain life. In a living cell, 
chemical reactions are constantly moving towards equilibrium, but never 
reach it. This is because a living cell is an open system. Materials pass in 
and out, the cell recycles the products of certain chemical reactions into 
other reactions, and chemical equilibrium is never reached. In this way, 
living organisms are in a constant energy-requiring, uphill battle against 
equilibrium and entropy. This constant supply of energy ultimately comes 
from sunlight, which is used to produce nutrients in the process of 
photosynthesis. 


Energy is released Energy is added 


reactants products 


Gibbs Free Energy 


> 
5 
- 
o 
< 
wi 
® 
oe 
J 
rs 
0 
2 
= 
o 


Exergonic and endergonic reactions result in changes in Gibbs 
free energy. Exergonic reactions release energy; endergonic 
reactions require energy to proceed. 


Energy in Living Systems 


Introduction 

"There is deposited in them (plants) an enormous quantity of potential energy, whose equivalent is 
provided to us as heat in the burning of a plant substance. So far as we know at present, the only 
living energy absorbed during plant growth are the rays of sunlight... Animals take up oxygen and 
complex oxidizable compounds made by plants, release largely as combustion products carbonic 
acid and water, ...thus using a certain amount of chemical potential energy to produce heat and 
mechanical forces." Hermann Ludwig Ferdinand von Helmholtz, 1847. 


Energy production within a cell involves many coordinated chemical pathways. Most of these 
pathways are combinations of oxidation and reduction reactions. Oxidation and reduction occur in 
tandem. An oxidation reaction strips an electron from an atom in a compound, and the addition of 
this electron to another compound is a reduction reaction. Because oxidation and reduction usually 
occur together, these pairs of reactions are called oxidation reduction reactions, or redox reactions. 


Electrons and Energy 


The removal of an electron from a molecule, oxidizing it, results in a decrease in potential energy 
in the oxidized compound. The electron (sometimes as part of a hydrogen atom), does not remain 
unbonded, however, in the cytoplasm of a cell. Rather, the electron is shifted to a second 
compound, reducing the second compound. The shift of an electron from one compound to another 
removes some potential energy from the first compound (the oxidized compound) and increases the 
potential energy of the second compound (the reduced compound)({link]). The transfer of electrons 
between molecules is important because most of the energy stored in atoms and used to fuel cell 
functions is in the form of high-energy electrons. The transfer of energy in the form of electrons 
allows the cell to transfer and use energy in an incremental fashion—in small packages rather than 
in a single, destructive burst. This section focuses on the extraction of energy from food; you will 
see that as you track the path of the transfers, you are tracking the path of electrons moving through 
metabolic pathways. 


uo!epIxO 
D1U061ax3 
Endergonic 
Reduction 


This image illustrates the coupling of oxidation and 
reduction reactions. Molecule B is being oxidized to a 
lower energy state while molecule D is being reduced to 
a higher energy state. (Image by Robert Bear) 


Electron Carriers 


In living systems, a small class of compounds functions as electron shuttles: They bind and carry 
high-energy electrons between compounds in pathways. The principal electron carriers we will 
consider are derived from the B vitamin group and are derivatives of nucleotides. These 
compounds can be easily reduced (that is, they accept electrons) or oxidized (they lose electrons). 
Nicotinamide adenine dinucleotide (NAD) ([link]) is derived from vitamin B3, niacin. NAD* is the 
oxidized form of the molecule; NADH is the reduced form of the molecule after it has accepted two 
electrons and a proton (which together are the equivalent of a hydrogen atom with an extra 
electron). 


NAD* can accept electrons from an organic molecule according to the general equation: 
Equation: 


RH * 
Reduci + ane —> See + - 
educin 
. ae Reduced Oxidized 
agent agent 


When electrons are added to a compound, they are reduced. A compound that reduces another is 
called a reducing agent. In the above equation, RH is a reducing agent, and NAD* is reduced to 
NADH. When electrons are removed from compound, it oxidized. A compound that oxidizes 


another is called an oxidizing agent. In the above equation, NAD* is an oxidizing agent, and RH is 
oxidized to R. 


Similarly, flavin adenine dinucleotide (FAD*) is derived from vitamin By, also called riboflavin. Its 
reduced form is FADH>. A second variation of NAD, NADP, contains an extra phosphate group. 
Both NAD* and FAD* are extensively used in energy extraction from sugars, and NADP plays an 
important role in anabolic reactions and photosynthesis. 


The oxidized form of the electron carrier (NAD*) is 
shown on the left and the reduced form (NADH) is 
shown on the right. The nitrogenous base in NADH has 
one more hydrogen ion and two more electrons than in 
NAD". 


Electron Transport Chain 


The energy associated with high energy electrons is harvested in an incremental fashion, and 
electron transport chains allow for this type of energy harvesting. An Electron Transport Chain is 
a series of membrane bound proteins that are specialized in shuttling electrons ({link]). An electron 
donor drops off high energy electrons and as the electrons pass from one protein to the next in the 
chain, a small amount of energy is released. The energy release by each step is then available to do 
work. After the electrons pass through the transport chain, the electrons are removed from the chain 
and attached to the final electron acceptor. As you will see later in this module, electron transport 
chains play an important role in the processes of photosynthesis and cellular respiration. 


anes edie 


Electron Donor Electron Acceptor 


This image illustrates the release of energy (noted as 
yellow and red stars) that is available to do work as 
electrons pass from one protein to another in the electron 
transport chain. (Image by Robert Bear) 


ATP in Living Systems 


A living cell cannot store significant amounts of free energy. Excess free energy would result in an 
increase of heat in the cell, which would result in excessive thermal motion that could damage and 
then destroy the cell. Rather, a cell must be able to handle that energy in a way that enables the cell 
to store energy safely and release it for use only as needed. Living cells accomplish this by using 
the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, 
and, like currency, this versatile compound can be used to fill any energy need of the cell. How? It 
functions similarly to a rechargeable battery. 


When ATP is broken down, usually by the removal of its terminal phosphate group, energy is 
released. The energy is used to do work by the cell, usually by the released phosphate binding to 
another molecule, activating it. For example, in the mechanical work of muscle contraction, ATP 
supplies the energy to move the contractile muscle proteins. Recall the active transport work of the 
sodium-potassium pump in the biological membranes. ATP alters the structure of the integral 
protein that functions as the pump, changing its affinity for sodium and potassium. In this way, the 
cell performs work, pumping ions against their electrochemical gradients. 


ATP Structure and Function 


At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an 
adenine molecule bonded to a ribose molecule and to a single phosphate group ([link]). Ribose is a 
five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a 
second phosphate group by a condensation reaction to this core molecule results in the formation of 
adenosine diphosphate (ADP); the addition of a third phosphate group by a condensation reaction 
forms adenosine triphosphate (ATP). 


Gamma Alpha 
phosphate phosphate aN 
group group N 
oe g 9 USN? 
—P—O—P—O—P— N 
| | in O 
oO O O 
Beta 
phosphate OH OH 
group : 
Ribose 


ATP (adenosine triphosphate) has three 
phosphate groups that can be removed by 
hydrolysis to form ADP (adenosine 
diphosphate) or AMP (adenosine 
monophosphate).The negative charges on 
the phosphate group naturally repel each 
other, requiring energy to bond them 
together and releasing energy when these 
bonds are broken. 


The addition of a phosphate group to a molecule requires energy. Phosphate groups are negatively 
charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. 
This repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two 

phosphate groups from ATP, a process called hydrolysis, releases energy. 


ATP Powers Cellular Work 


Hydrolysis is the process of breaking complex macromolecules apart. During hydrolysis, water is 
split, or lysed, and the resulting hydrogen atom (H*) and a hydroxy] group (OH) are added to the 
larger molecule. The hydrolysis of ATP produces ADP, together with an inorganic phosphate ion 
(P;), and the release of free energy an exergonic reaction. This free energy is then available to drive 
an endergonic reaction. The release of energy and absorption of this free energy is a coupled 
reaction. To carry out life processes, ATP is continuously broken down into ADP, and like a 
rechargeable battery, ADP is continuously regenerated into ATP by the reattachment of a third 
phosphate group by a condensation reaction ([link]). Water, which was broken down into its 
hydrogen atom and hydroxyl group during ATP hydrolysis, is reformed when a third phosphate is 
added to the ADP molecule, reforming ATP with energy being absorbed. The energy necessary for 
driving the formation of ATP comes from an exergonic reaction. Once again the coupling of an 
exergonic reaction drives an endergonic reaction or the formation of ATP. 


sIsA|OJpAH 
1U0B1axy 
Endergonic 


— 
m — 

iS 
an i 
Te} aD 
fe) oO 
242 
a uo 


This image illustrates the ATP cycle and how ATP couples the release of energy from one 
reaction and makes that energy available for cellular work or endergonic reactions. (Image by 
Robert Bear) 


Obviously, energy must be infused into the system to regenerate ATP. Where does this energy come 
from? In nearly every living thing on earth, the energy comes from the metabolism of glucose. In 
this way, ATP is a direct link between the limited set of exergonic pathways of glucose catabolism 
and the multitude of endergonic pathways that power living cells. 


Phosphorylation 


Recall that, in some chemical reactions, enzymes may bind to several substrates that react with 
each other on the enzyme, forming an intermediate complex. An intermediate complex is a 
temporary structure, and it allows one of the substrates (such as ATP) and reactants to more readily 
react with each other; in reactions involving ATP, ATP is one of the substrates and ADP is a 
product. During an endergonic chemical reaction, ATP forms an intermediate complex with the 
substrate and enzyme in the reaction. This intermediate complex allows the ATP to transfer its third 
phosphate group, with its energy, to the substrate, a process called phosphorylation. 
Phosphorylation refers to the addition of the phosphate (~P). This is illustrated by the following 
generic reaction: 

Equation: 


A+ enzyme + ATP > [A — enzyme — ~P] — B+ enzyme + ADP + phosphate ion 


When the intermediate complex breaks apart, the energy is used to modify the substrate and convert 
it into a product of the reaction. The ADP molecule and a free phosphate ion are released into the 


medium and are available for recycling through cell metabolism. 


Substrate Phosphorylation 


ATP is generated through two mechanisms during the breakdown of glucose. A few ATP molecules 
are generated (that is, regenerated from ADP) as a direct result of the chemical reactions that occur 
in the catabolic pathways. A phosphate group is removed from an intermediate reactant in the 
pathway, and the free energy of the reaction is used to add the third phosphate to an available ADP 
molecule, producing ATP ({link]). This very direct method of phosphorylation is called substrate- 
level phosphorylation. 


In phosphorylation reactions, the gamma 
phosphate of ATP is attached to a protein. 


Oxidative Phosphorylation 


Most of the ATP generated during glucose catabolism, however, is derived from a much more 
complex process, chemiosmosis, which takes place in mitochondria ([link]) within a eukaryotic cell 
or the plasma membrane of a prokaryotic cell. Chemiosmosis, a process of ATP production in 
cellular metabolism, is used to generate 90 percent of the ATP made during glucose catabolism and 
is also the method used in the light reactions of photosynthesis to harness the energy of sunlight. 
The production of ATP using the process of chemiosmosis is called oxidative phosphorylation 
because of the involvement of oxygen in the process. 


ATP synthase enzymes and the 
electron transport chain are 
embedded in the inner membrane. 


Intermembrane space 
Matrix 


Inner membrane 
Outer membrane 


In eukaryotes, oxidative 
phosphorylation takes place in 
mitochondria. In prokaryotes, 
this process takes place in the 

plasma membrane. (Credit: 
modification of work by 

Mariana Ruiz Villareal) 


Cell Membranes and Passive Transport 


Introduction 

" A vital phenomenon can only be regarded as explained if it has been 
proven that it appears as the result of the material components of living 
organisms interacting according to the laws which those same components 
follow in their interactions outside of living systems. " A. E. Fick, German 
physiologist who developed the first mathematical explanation of diffusion 


The simple diffusion model developed by Fick does indeed explain the 
movement of molecules in both living and non-living systems. Molecules 
move freely from an area of higher concentration to and area of lower 
concentration, according to Fick's Law. Living organisms, however, impose 
a barrier to diffusion of molecules into and from their cells - the plasma 
membrane which surrounds all cells. Plasma membranes must allow certain 
substances to enter and leave a cell, and prevent some harmful materials 
from entering and some essential materials from leaving. In other words, 
plasma membranes are selectively permeable—they allow some 
substances to pass through, but not others. If they were to lose this 
selectivity, the cell would no longer be able to sustain itself, and it would be 
destroyed. Some cells require larger amounts of specific substances than do 
other cells; they must have a way of obtaining these materials from 
extracellular fluids. This may happen passively, as certain materials move 
back and forth, or the cell may have special mechanisms that facilitate 
transport. Some materials are so important to a cell that it spends some of 
its energy, hydrolyzing adenosine triphosphate (ATP), to obtain these 
materials. Red blood cells use some of their energy doing just that. All cells 
spend the majority of their energy to maintain an imbalance of sodium and 
potassium ions between the interior and exterior of the cell. 


The most direct forms of membrane transport are passive. Passive 
transport is a naturally occurring phenomenon and does not require the cell 
to exert any of its energy to accomplish the movement. In passive transport, 
substances move from an area of higher concentration to an area of lower 
concentration. A physical space in which there is a range of concentrations 
of a single substance is said to have a concentration gradient. 


Selective Permeability 


Plasma membranes are asymmetric: the interior of the membrane is not 
identical to the exterior of the membrane. In fact, there is a considerable 
difference between the array of phospholipids and proteins between the two 
leaflets that form a membrane. On the interior of the membrane, some 
proteins serve to anchor the membrane to fibers of the cytoskeleton. There 
are peripheral proteins on the exterior of the membrane that bind elements 
of the extracellular matrix. Carbohydrates, attached to lipids or proteins, are 
also found on the exterior surface of the plasma membrane. These 
carbohydrate complexes help the cell bind substances that the cell needs in 
the extracellular fluid. This adds considerably to the selective nature of 
plasma membranes ((Link]). 


Glycoprotein: protein with Glycolipid: lipid with 
| carbohydrate attached rh carbohydrate 
attached 


Peripheral membrane Phospholipid 
protein bilayer 
Integral membrane ali Protein channel 
protein 


Cytoskeletal filaments 


The exterior surface of the plasma membrane is not identical to the 
interior surface of the same membrane. 


Recall that plasma membranes are amphiphilic: They have hydrophilic and 
hydrophobic regions. This characteristic helps the movement of some 
materials through the membrane and hinders the movement of others. 


Lipid-soluble material with a low molecular weight can easily slip through 
the hydrophobic lipid core of the membrane. Substances such as the fat- 
soluble vitamins A, D, E, and K readily pass through the plasma 
membranes in the digestive tract and other tissues. Fat-soluble drugs and 
hormones also gain easy entry into cells and are readily transported into the 
body’s tissues and organs. Molecules of oxygen and carbon dioxide have no 
charge and so pass through membranes by simple diffusion. 


Polar substances present problems for the membrane. While some polar 
molecules connect easily with the outside of a cell, they cannot readily pass 
through the lipid core of the plasma membrane. Additionally, while small 
ions could easily slip through the spaces in the mosaic of the membrane, 
their charge prevents them from doing so. Ions such as sodium, potassium, 
calcium, and chloride must have special means of penetrating plasma 
membranes. Simple sugars and amino acids also need help with transport 
across plasma membranes, achieved by various transmembrane proteins 
(channels). 


Diffusion 


Diffusion is a passive process of transport. A single substance tends to 
move from an area of high concentration to an area of low concentration 
until the concentration is equal across a space. You are familiar with 
diffusion of substances through the air. For example, think about someone 
opening a bottle of ammonia in a room filled with people. The ammonia gas 
is at its highest concentration in the bottle; its lowest concentration is at the 
edges of the room. The ammonia vapor will diffuse, or spread away, from 
the bottle, and gradually, more and more people will smell the ammonia as 
it spreads. Materials move within the cell’s cytosol by diffusion, and certain 
materials move through the plasma membrane by diffusion ([link]). 
Diffusion expends no energy. On the contrary, concentration gradients are a 
form of potential energy, dissipated as the gradient is eliminated. 


Lipid bilayer 
(plasma 


membrane) 


Time 


Diffusion through a permeable membrane moves a substance from an 
area of high concentration (extracellular fluid, in this case) down its 
concentration gradient (into the cytoplasm). (credit: modification of 

work by Mariana Ruiz Villareal) 


Each separate substance in a medium, such as the extracellular fluid, has its 
own concentration gradient, independent of the concentration gradients of 
other materials. In addition, each substance will diffuse according to that 
gradient. Within a system, there will be different rates of diffusion of the 
different substances in the medium. 


Factors That Affect Diffusion 


Molecules move constantly in a random manner, at a rate that depends on 
their mass, their environment, and the amount of thermal energy they 
possess, which in turn is a function of temperature. This movement 
accounts for the diffusion of molecules through whatever medium in which 
they are localized. A substance will tend to move into any space available 
to it until it is evenly distributed throughout it. After a substance has 
diffused completely through a space, removing its concentration gradient, 
molecules will still move around in the space, but there will be no net 


movement of the number of molecules from one area to another. This lack 
of a concentration gradient in which there is no net movement of a 
substance is known as dynamic equilibrium. While diffusion will go 
forward in the presence of a concentration gradient of a substance, several 
factors affect the rate of diffusion. 


e Extent of the concentration gradient: The greater the difference in 
concentration, the more rapid the diffusion. The closer the distribution 
of the material gets to equilibrium, the slower the rate of diffusion 
becomes. 

e Mass of the molecules diffusing: Heavier molecules move more 
slowly; therefore, they diffuse more slowly. The reverse is true for 
lighter molecules. 

e Temperature: Higher temperatures increase the energy and therefore 
the movement of the molecules, increasing the rate of diffusion. Lower 
temperatures decrease the energy of the molecules, thus decreasing the 
rate of diffusion. 

e Solvent density: As the density of a solvent increases, the rate of 
diffusion decreases. The molecules slow down because they have a 
more difficult time getting through the denser medium. If the medium 
is less dense, diffusion increases. Because cells primarily use diffusion 
to move materials within the cytoplasm, any increase in the 
cytoplasm’s density will inhibit the movement of the materials. An 
example of this is a person experiencing dehydration. As the body’s 
cells lose water, the rate of diffusion decreases in the cytoplasm, and 
the cells’ functions deteriorate. Neurons tend to be very sensitive to 
this effect. Dehydration frequently leads to unconsciousness and 
possibly coma because of the decrease in diffusion rate within the 
cells. 

e Solubility: As discussed earlier, nonpolar or lipid-soluble materials 
pass through plasma membranes more easily than polar materials, 
allowing a faster rate of diffusion. 

e Surface area and thickness of the plasma membrane: Increased surface 
area increases the rate of diffusion, whereas a thicker membrane 
reduces it. 

e Distance travelled: The greater the distance that a substance must 
travel, the slower the rate of diffusion. This places an upper limitation 


on cell size. A large, spherical cell will die because nutrients or waste 
cannot reach or leave the center of the cell, respectively. Therefore, 
cells must either be small in size, as in the case of many prokaryotes, 
or be flattened, as with many single-celled eukaryotes. 


A variation of diffusion is the process of filtration. In filtration, material 
moves according to its concentration gradient through a membrane; 
sometimes the rate of diffusion is enhanced by pressure, causing the 
substances to filter more rapidly. This occurs in the kidney, where blood 
pressure forces large amounts of water and accompanying dissolved 
substances, or solutes, out of the blood and into the renal tubules. The rate 
of diffusion in this instance is almost totally dependent on pressure. One of 
the effects of high blood pressure is the appearance of protein in the urine, 
which is “squeezed through” by the abnormally high pressure. 


Facilitated diffusion 


In facilitated diffusion, also called facilitated transport, materials diffuse 
across the plasma membrane with the help of membrane proteins. A 
concentration gradient exists that would allow these materials to diffuse into 
the cell without expending cellular energy. However, these materials are 
ions or polar molecules that are repelled by the hydrophobic parts of the 
biological membrane. Facilitated diffusion proteins shield these materials 
from the repulsive force of the membrane, allowing them to diffuse into the 
cell. 


The material being transported is first attached to protein or glycoprotein 
receptors on the exterior surface of the plasma membrane. This allows the 
material that is needed by the cell to be removed from the extracellular 
fluid. The substances are then passed to specific integral proteins that 
facilitate their passage. Some of these integral proteins are collections of 
beta pleated sheets that form a pore or channel through the phospholipid 
bilayer. Others are carrier proteins which bind with the substance and aid its 
diffusion through the membrane. 


Channels 


The integral proteins involved in facilitated diffusion are collectively 
referred to as transport proteins, and they function as either channels for 
the material or carriers. In both cases, they are transmembrane proteins. 
Channels are specific for the substance that is being transported. Channel 
proteins have hydrophilic domains exposed to the intracellular and 
extracellular fluids; they additionally have a hydrophilic channel through 
their core that provides a hydrated opening through the membrane layers 
({link]). Passage through the channel allows polar compounds to avoid the 
nonpolar central layer of the plasma membrane that would otherwise slow 
or prevent their entry into the cell. Aquaporins are channel proteins that 
allow water to pass through the membrane at a very high rate. 


Extracellular fluid 
OQ e ®@ 
e O 
O @ e 
Oo 


Protein 
channel 


_ al Anant 
a 


Cytoplasm 


Facilitated diffusion moves 
substances down their 
concentration gradients. They may 
cross the plasma membrane with 
the aid of channel proteins. (credit: 
modification of work by Mariana 
Ruiz Villareal) 


Channel proteins are either open at all times or they are “gated,” which 
controls the opening of the channel. The attachment of a particular ion to 
the channel protein may control the opening, or other mechanisms or 
substances may be involved. In some tissues, sodium and chloride ions pass 
freely through open channels, whereas in other tissues a gate must be 
opened to allow passage. An example of this occurs in the kidney, where 
both forms of channels are found in different parts of the renal tubules. 
Cells involved in the transmission of electrical impulses, such as nerve and 
muscle cells, have gated channels for sodium, potassium, and calcium in 
their membranes. Opening and closing of these channels changes the 
relative concentrations on opposing sides of the membrane of these ions, 
resulting in the facilitation of electrical transmission along membranes (in 
the case of nerve cells) or in muscle contraction (in the case of muscle 
cells). 


Carrier Proteins 


Another type of protein embedded in the plasma membrane is a carrier 
protein. This aptly named protein binds a substance and, in doing so, 
triggers a change of its own shape, moving the bound molecule from the 
outside of the cell to its interior ({link]); depending on the gradient, the 
material may move in the opposite direction. Carrier proteins are typically 
specific for a single substance. This selectivity adds to the overall 
selectivity of the plasma membrane. The exact mechanism for the change of 
shape is poorly understood. Proteins can change shape when their hydrogen 
bonds are affected, but this may not fully explain this mechanism. Each 
carrier protein is specific to one substance, and there are a finite number of 
these proteins in any membrane. This can cause problems in transporting 
enough of the material for the cell to function properly. When all of the 
proteins are bound to their ligands, they are saturated and the rate of 
transport is at its maximum. Increasing the concentration gradient at this 
point will not result in an increased rate of transport. 


Extracellular fluid 
ae) Oo 
O ® @ 
e) e® © O 
e - 


Seeing ong mnt mn 


Weduuu ee Wuut 


Carrier 


roteins 
e) @ P e @ 


1) ad Cytoplasm 


Some substances are able to move down their concentration gradient 

across the plasma membrane with the aid of carrier proteins. Carrier 

proteins change shape as they move molecules across the membrane. 
(credit: modification of work by Mariana Ruiz Villareal) 


An example of this process occurs in the kidney. Glucose, water, salts, ions, 
and amino acids needed by the body are filtered in one part of the kidney. 
This filtrate, which includes glucose, is then reabsorbed in another part of 
the kidney. Because there are only a finite number of carrier proteins for 
glucose, if more glucose is present than the proteins can handle, the excess 
is not transported and it is excreted from the body in the urine. In a diabetic 
individual, this is described as “spilling glucose into the urine.” A different 
group of carrier proteins called glucose transport proteins, or GLUTs, are 
involved in transporting glucose and other hexose sugars through plasma 
membranes within the body. 


Channel and carrier proteins transport material at different rates. Channel 
proteins transport much more quickly than do carrier proteins. Channel 
proteins facilitate diffusion at a rate of tens of millions of molecules per 
second, whereas carrier proteins work at a rate of a thousand to a million 
molecules per second. 


Osmosis 


Osmosis is the movement of water through a semipermeable membrane 
according to the concentration gradient of water across the membrane, 
which is inversely proportional to the concentration of solutes. While 
diffusion transports material across membranes and within cells, osmosis 
transports only water across a membrane and the membrane limits the 
diffusion of solutes in the water. Not surprisingly, the aquaporins that 
facilitate water movement play a large role in osmosis, most prominently in 
red blood cells and the membranes of kidney tubules. 


Mechanism 


Osmosis is a special case of diffusion. Water, like other substances, moves 
from an area of high concentration to one of low concentration. An obvious 
question is what makes water move at all? Imagine a beaker with a 
semipermeable membrane separating the two sides or halves ([link]). On 
both sides of the membrane the water level is the same, but there are 
different concentrations of a dissolved substance, or solute, that cannot 
cross the membrane (otherwise the concentrations on each side would be 
balanced by the solute crossing the membrane). If the volume of the 
solution on both sides of the membrane is the same, but the concentrations 
of solute are different, then there are different amounts of water, the solvent, 
on either side of the membrane. 


Semipermeable membrane 


In osmosis, water always moves 
from an area of higher water 
concentration to one of lower 
concentration. In the diagram 
shown, the solute cannot pass 

through the selectively permeable 
membrane, but the water can. 


To illustrate this, imagine two full glasses of water. One has a single 
teaspoon of sugar in it, whereas the second one contains one-quarter cup of 
sugar. If the total volume of the solutions in both cups is the same, which 
cup contains more water? Because the large amount of sugar in the second 
cup takes up much more space than the teaspoon of sugar in the first cup, 
the first cup has more water in it. 


Returning to the beaker example, recall that it has a mixture of solutes on 
either side of the membrane. A principle of diffusion is that the molecules 
move around and will spread evenly throughout the medium if they can. 
However, only the material capable of getting through the membrane will 
diffuse through it. In this example, the solute cannot diffuse through the 
membrane, but the water can. Water has a concentration gradient in this 
system. Thus, water will diffuse down its concentration gradient, crossing 
the membrane to the side where it is less concentrated. This diffusion of 
water through the membrane—osmosis—will continue until the 
concentration gradient of water goes to zero or until the hydrostatic pressure 
of the water balances the osmotic pressure. Osmosis proceeds constantly in 
living systems. 


Tonicity 


Tonicity is a measure of the osmotic pressure of two solutions separated by 
a semipermeable membrane. So, tonicity describes how an extracellular 
solution can change the volume of a cell by affecting osmosis. A solution's 
tonicity often directly correlates with the osmolarity of the solution. 
Osmolarity describes the total solute concentration of the solution. A 


solution with low osmolarity has a greater number of water molecules 
relative to the number of solute particles; a solution with high osmolarity 
has fewer water molecules with respect to solute particles. In a situation in 
which solutions of two different osmolarities are separated by a membrane 
permeable to water, though not to the solute, water will move from the side 
of the membrane with lower osmolarity (and more water) to the side with 
higher osmolarity (and less water). This effect makes sense if you 
remember that the solute cannot move across the membrane, and thus the 
only component in the system that can move—the water—moves along its 
own concentration gradient. An important distinction that concerns living 
systems is that osmolarity measures the number of particles (which may be 
molecules) in a solution. Therefore, a solution that is cloudy with cells may 
have a lower osmolarity than a solution that is clear, if the second solution 
contains more dissolved molecules than there are cells. 


Hypotonic Solutions 


Three terms—hypotonic, isotonic, and hypertonic—are used to relate the 
osmolarity of a cell to the osmolarity of the extracellular fluid that contains 
the cells. In a hypotonic situation, the extracellular fluid has lower 
osmolarity than the fluid inside the cell, and water enters the cell. (In living 
systems, the point of reference is always the cytoplasm, so the prefix hypo- 
means that the extracellular fluid has a lower concentration of solutes, or a 
lower osmolarity, than the cell cytoplasm.) It also means that the 
extracellular fluid has a higher concentration of water in the solution than 
does the cell. In this situation, water will follow its concentration gradient 
and enter the cell. 


Hypertonic Solutions 


As for a hypertonic solution, the prefix hyper- refers to the extracellular 
fluid having a higher osmolarity than the cell’s cytoplasm; therefore, the 
fluid contains less water than the cell does. Because the cell has a relatively 
higher concentration of water, water will leave the cell. 


Isotonic Solutions 


In an isotonic solution, the extracellular fluid has the same osmolarity as 
the cell. If the osmolarity of the cell matches that of the extracellular fluid, 
there will be no net movement of water into or out of the cell, although 
water will still move in and out. Blood cells and plant cells in hypertonic, 
isotonic, and hypotonic solutions take on characteristic appearances ({link]). 


Hypertonic Isotonic Hypotonic 
—e Ss *@® 


Osmotic pressure changes the 
shape of red blood cells in 
hypertonic, isotonic, and 
hypotonic solutions. (credit: 
Mariana Ruiz Villareal) 


Tonicity in Living Systems 


In a hypotonic environment, water enters a cell, and the cell swells. In an 
isotonic condition, the relative concentrations of solute and solvent are 
equal on both sides of the membrane. There is no net water movement; 
therefore, there is no change in the size of the cell. In a hypertonic solution, 
water leaves a cell and the cell shrinks. If either the hypo- or hyper- 
condition goes to excess, the cell’s functions become compromised, and the 
cell may be destroyed. 


A red blood cell will burst, or lyse, when it swells beyond the plasma 
membrane’s capability to expand. Remember, the membrane resembles a 
mosaic, with discrete spaces between the molecules composing it. If the cell 
swells, and the spaces between the lipids and proteins become too large, the 
cell will break apart. 


In contrast, when excessive amounts of water leave a red blood cell, the cell 
shrinks, or crenates. This has the effect of concentrating the solutes left in 
the cell, making the cytosol denser and interfering with diffusion within the 
cell. The cell’s ability to function will be compromised and may also result 
in the death of the cell. 


Various living things have ways of controlling the effects of osmosis—a 
mechanism called osmoregulation. Some organisms, such as plants, fungi, 
bacteria, and some protists, have cell walls that surround the plasma 
membrane and prevent cell lysis in a hypotonic solution. The plasma 
membrane can only expand to the limit of the cell wall, so the cell will not 
lyse. In fact, the cytoplasm in plants is always slightly hypertonic to the 
cellular environment, and water will always enter a cell if water is 
available. This inflow of water produces turgor pressure, which stiffens the 
cell walls of the plant ({link]). In nonwoody plants, turgor pressure supports 
the plant. Conversly, if the plant is not watered, the extracellular fluid will 
become hypertonic, causing water to leave the cell. In this condition, the 
cell does not shrink because the cell wall is not flexible. However, the 
plasma membrane detaches from the wall and constricts the cytoplasm. This 
is called plasmolysis. Plants lose turgor pressure in this condition and wilt 
({link]). 


Hypertonic lsotonic Hypotonic 


Vacuole 


HO 


The turgor pressure within a plant 
cell depends on the tonicity of the 


solution that it is bathed in. 
(credit: modification of work by 
Mariana Ruiz Villareal) 


Without adequate water, the plant on the left has lost turgor pressure, 
visible in its wilting; the turgor pressure is restored by watering it 
(right). (credit: Victor M. Vicente Selvas) 


Tonicity is a concern for all living things. For example, paramecia and 
amoebas, which are protists that lack cell walls, have contractile vacuoles. 
This vesicle collects excess water from the cell and pumps it out, keeping 
the cell from lysing as it takes on water from its environment ((Link]). 


Contractile 
vacuoles 


A paramecium’s contractile vacuole, 
here visualized using bright field light 
microscopy at 480x magnification, 
continuously pumps water out of the 
organism’s body to keep it from 
bursting in a hypotonic medium. 
(credit: modification of work by NIH; 
scale-bar data from Matt Russell) 


Many marine invertebrates have internal salt levels matched to their 
environments, making them isotonic with the water in which they live. Fish, 
however, must spend approximately five percent of their metabolic energy 
maintaining osmotic homeostasis. Freshwater fish live in an environment 
that is hypotonic to their cells. These fish actively take in salt through their 
gills and excrete diluted urine to rid themselves of excess water. Saltwater 
fish live in the reverse environment, which is hypertonic to their cells, and 
they secrete salt through their gills and excrete highly concentrated urine. 


In vertebrates, the kidneys regulate the amount of water in the body. 
Osmoreceptors are specialized cells in the brain that monitor the 
concentration of solutes in the blood. If the levels of solutes increase 
beyond a certain range, a hormone is released that retards water loss 
through the kidney and dilutes the blood to safer levels. Animals also have 
high concentrations of albumin, which is produced by the liver, in their 
blood. This protein is too large to pass easily through plasma membranes 
and is a major factor in controlling the osmotic pressures applied to tissues. 


Energy Requiring Transport 


Introduction 

"Against the wind," "We were runnin’ against the wind," "We were young 
and strong and we were runnin" "against the wind" - Bob Seger, chorus of 
Against the Wind. 


Active Transport 


As the song says, you have to be strong to be moving against the wind. 
And, at the cellular level, you have to have significant energy to move 
materials against a concentration gradient. The process which cells use to 
do that is called active transport. Active transport mechanisms require the 
use of the cell’s energy, usually in the form of adenosine triphosphate 
(ATP). If a substance must move into the cell against its concentration 
gradient, that is, if the concentration of the substance inside the cell must be 
greater than its concentration in the extracellular fluid, the cell must use 
energy to move the substance. Some active transport mechanisms move 
small-molecular weight material, such as ions, through the membrane. 


In addition to moving small ions and molecules through the membrane, 
cells also need to remove and take in larger molecules and particles. Some 
cells are even capable of engulfing entire unicellular microorganisms. You 
might have correctly hypothesized that the uptake and release of large 
particles by the cell requires energy. A large particle, however, cannot pass 
through the membrane, even with energy supplied by the cell. 


Electrochemical Gradient 


We have discussed simple concentration gradients—differential 
concentrations of a substance across a space or a membrane—but in living 
systems, gradients are more complex. Because cells contain proteins, most 
of which are negatively charged, and because ions move into and out of 
cells, there is an electrical gradient, a difference of charge, across the 
plasma membrane. The interior of living cells is electrically negative with 
respect to the extracellular fluid in which they are bathed; at the same time, 
cells have higher concentrations of potassium (K*) and lower 


concentrations of sodium (Na‘) than does the extracellular fluid. Thus, in a 
living cell, the concentration gradient and electrical gradient of Na* 
promotes diffusion of the ion into the cell, and the electrical gradient of Na* 
(a positive ion) tends to drive it inward to the negatively charged interior. 
The situation is more complex, however, for other elements such as 
potassium. The electrical gradient of K* promotes diffusion of the ion into 
the cell, but the concentration gradient of K* promotes diffusion out of the 
cell ({link]). The combined gradient that affects an ion is called its 
electrochemical gradient, and it is especially important to muscle and 
nerve cells. 


kj Net Charge — 


Electrochemical gradients arise from the 
combined effects of concentration gradients and 
electrical gradients. (credit: modification of 
work by “Synaptitude”/Wikimedia Commons) 


Moving Against a Gradient 


To move substances against a concentration or an electrochemical gradient, 
the cell must use energy. This energy is harvested from ATP that is 
generated through cellular metabolism. Active transport mechanisms, 
collectively called pumps or carrier proteins, work against electrochemical 
gradients. With the exception of ions, small substances constantly pass 
through plasma membranes. Active transport maintains concentrations of 
ions and other substances needed by living cells in the face of these passive 
changes. Much of a cell’s supply of metabolic energy may be spent 
maintaining these processes. Because active transport mechanisms depend 
on cellular metabolism for energy, they are sensitive to many metabolic 
poisons that interfere with the supply of ATP. 


Two mechanisms exist for the transport of small-molecular weight material 
and macromolecules. Primary active transport moves ions across a 
membrane and creates a difference in charge across that membrane. The 
primary active transport system uses ATP to move a substance, such as an 
ion, into the cell, and often at the same time, a second substance is moved 
out of the cell. The sodium-potassium pump, an important pump in animal 
cells, expends energy to move potassium ions into the cell and a different 
number of sodium ions out of the cell ({link]). The action of this pump 
results in a concentration and charge difference across the membrane. 


Extracellular space 


@ QO Na* 
. @ 
ons Q @ oe: “ @ 
e. 78 @ @ 


coe] AGRON TOOT Ti 
- oF HUE ULL UU 


Phosphate ““@ 
od 
. e 


Cytoplasm K* 


The sodium-potassium pump move potassium and sodium ions 
across the plasma membrane. (credit: modification of work by 


Mariana Ruiz Villarreal) 


Secondary active transport describes the movement of material using the 
energy of the electrochemical gradient established by primary active 
transport. Using the energy of the electrochemical gradient created by the 
primary active transport system, other substances such as amino acids and 
glucose can be brought into the cell through membrane channels. ATP itself 
is formed through secondary active transport using a hydrogen ion gradient 
in the mitochondrion. 


Bulk Transport of Materials 


Endocytosis 


Endocytosis is a type of energy requiring transport that moves particles, 
such as large molecules, parts of cells, and even whole cells, into a cell. 
There are different variations of endocytosis, but all share a common 
characteristic: The plasma membrane of the cell invaginates, forming a 
pocket around the target particle. The pocket pinches off, resulting in the 
particle being contained in a newly created vacuole that is formed from the 
plasma membrane. 


Phagocytosis Pinocytosis Receptor-mediated 


endocytosis 


coed 


s 
" » * 
rs Large particle * 
P . x" * 
A 
Plasma 
membrane 
Clathrin Receptor 


© 


Vacuole 


©... 
Coated vesicle 


(a) (b) (©) 


Three variations of endocytosis are shown. (a) In one form of 
endocytosis, phagocytosis, the plasma membrane surrounds the 
particle and pinches off to form an intracellular vacuole. (b) In 

another type of endocytosis, pinocytosis, the cell membrane 

surrounds a small volume of fluid and pinches off, forming a 

vesicle. (c) In receptor-mediated endocytosis, uptake of substances 
by the cell is targeted to a single type of substance that binds at the 
receptor on the plasma membrane. (credit: modification of work 
by Mariana Ruiz Villarreal) 


Phagocytosis is the process by which large particles, such as cells, are 
taken in by a cell. For example, when microorganisms invade the human 
body, a type of white blood cell called a neutrophil removes the invader 
through this process, surrounding and engulfing the microorganism, which 
is then destroyed by the neutrophil ((link]). 


A variation of endocytosis is called pinocytosis. This literally means “cell 
drinking” and was named at a time when the assumption was that the cell 

was purposefully taking in extracellular fluid. In reality, this process takes 
in solutes that the cell needs from the extracellular fluid ((link]). 


A targeted variation of endocytosis employs binding proteins in the plasma 
membrane that are specific for certain substances ({link]). The particles 
bind to the proteins and the plasma membrane invaginates, bringing the 
substance and the proteins into the cell. If passage across the membrane of 
the target of receptor-mediated endocytosis is ineffective, it will not be 
removed from the tissue fluids or blood. Instead, it will stay in those fluids 
and increase in concentration. Some human diseases are caused by a failure 
of receptor-mediated endocytosis. For example, the form of cholesterol 
termed low-density lipoprotein or LDL (also referred to as “bad” 
cholesterol) is removed from the blood by receptor-mediated endocytosis. 
In the human genetic disease familial hypercholesterolemia, the LDL 
receptors are defective or missing entirely. People with this condition have 
life-threatening levels of cholesterol in their blood, because their cells 
cannot clear the chemical from their blood. 


Exocytosis 


In contrast to these methods of moving material into a cell is the process of 
exocytosis. Exocytosis is the opposite of the processes discussed above in 
that its purpose is to expel material from the cell into the extracellular fluid. 
A particle enveloped in membrane fuses with the interior of the plasma 
membrane. This fusion opens the membranous envelope to the exterior of 
the cell, and the particle is expelled into the extracellular space ([link]). 


Exocytosis 


Extracellular fluid 


SS Cyctoplasm 


Vesicle 


In exocytosis, a vesicle 

migrates to the plasma 

membrane, binds, and 
releases its contents to the 
outside of the cell. (credit: 
modification of work by 
Mariana Ruiz Villarreal) 


Overview of Photosynthesis 


Introduction 

"Nature has put itself the problem how to catch in flight light streaming to 
the earth and to store the most elusive of all powers in rigid form. To 
achieve this aim, it has covered the crust of earth with organisms which in 
their life processes absorb the light of the sun and use this power to produce 
a continuously accumulating chemical difference. ... The plants take in one 
form of power, light; and produce another power, chemical difference. " 
Robert Mayer, German physicist who developed the concept of the 
conservation of heat, 1845 


The sun not only provides the energy for the plants themselves, but for all 
other creatures on the planet. Indeed, ancient photosynthesis provided the 
fossil fuel energy that we use to generate electricity or power our cars. Each 
cell in every organism runs on the chemical energy found mainly in 
carbohydrate molecules (food), and the majority of these molecules are 
produced by one process: photosynthesis. Through photosynthesis, certain 
organisms convert solar energy (sunlight) into chemical energy, which is 
then used to build carbohydrate molecules. The energy used to hold these 
molecules together is released when an organism breaks down food during 
cellular respiration. Cells then use this energy to perform work, such as 
movement. 


The energy that is harnessed from photosynthesis enters the ecosystems of 
our planet continuously and is transferred from one organism to another 
until almost all of the harvested energy is transferred and released as heat 
energy. Therefore, directly or indirectly, the process of photosynthesis 
provides most of the energy required by living things on earth ((link]). 


Co, 


Glucose ad 
Sunlight--> t= ae ==> Heat 


Autotrophs Heterotrophs 


/ 
4 


be HO 


Heat 


This image shows the role of photosynthesis is the flow of energy 
through and ecosystem. Light energy enters the system through 
photosynthesis and leaves primarily as heat energy once the energy is 
used by organisms. (image by Eva Horne and Robert Bear) 


Photosynthesis also results in the release of oxygen into the atmosphere. In 
short, to eat and breathe, humans depend almost entirely on the organisms 
that carry out photosynthesis. 


Solar Dependence and Food Production 


Some organisms can carry out photosynthesis, whereas others cannot. An 
autotroph is an organism that can produce its own food. The Greek roots of 
the word autotroph mean “self” (auto) “feeder” (troph). Plants are the best- 
known autotrophs, but others exist, including certain types of bacteria and 
algae ({link]). Oceanic algae contribute enormous quantities of food and 
oxygen to global food chains. Plants are also photoautotrophs, a type of 
autotroph that uses sunlight and carbon from carbon dioxide to synthesize 
chemical energy in the form of carbohydrates. All organisms carrying out 
photosynthesis require sunlight. 


2 See 


(a) (b) (c) 


(a) Plants, (b) algae, and (c) certain bacteria, called cyanobacteria, are 
photoautotrophs that can carry out photosynthesis. Algae can grow 
Over enormous areas in water, at times completely covering the 
surface. (credit a: Steve Hillebrand, U.S. Fish and Wildlife Service; 
credit b: "eutrophication&hypoxia"/Flickr; credit c: NASA; scale-bar 
data from Matt Russell) 


Heterotrophs are organisms incapable of photosynthesis that must 
therefore obtain energy and carbon from food by consuming other 
organisms. The Greek roots of the word heterotroph mean “other” (hetero) 
“feeder” (troph), meaning that their food comes from other organisms. Even 
if the food organism is another animal, this food traces its origins back to 
autotrophs and the process of photosynthesis. Humans are heterotrophs, as 
are all animals. Heterotrophs depend on autotrophs, either directly or 
indirectly. Deer and wolves are heterotrophs. A deer obtains energy by 
eating plants. A wolf eating a deer obtains energy that originally came from 
the plants eaten by that deer. The energy in the plant came from 
photosynthesis, and therefore it is the only autotroph in this example. Using 
this reasoning, all food eaten by humans also links back to autotrophs that 
carry out photosynthesis. 


The Flow of Energy 


Whether the organism is a bacterium, plant, or animal, all living things 
access energy by breaking down carbohydrate molecules. But if plants 
make carbohydrate molecules, why would they need to break them down, 
especially when it has been shown that the gas organisms release as a 


“waste product” (CO>) acts as a substrate for the formation of more food in 
photosynthesis? Remember, living things need energy to perform life 
functions. In addition, an organism can either make its own food or eat 
another organism—either way, the food still needs to be broken down. 
Finally, in the process of breaking down food, called cellular respiration, 
heterotrophs release needed energy and produce “waste” in the form of CO» 
gas. 


In nature, there is no such thing as waste. Every single atom of matter and 
energy is conserved, recycling over and over infinitely. Substances change 
form or move from one type of molecule to another, but their constituent 
atoms never disappear. 


CO, is no more a form of waste than oxygen is form of waste from 
photosynthesis. Both are byproducts of reactions and move on to other 
reactions. Photosynthesis absorbs light energy to build carbohydrates in 
chloroplasts, and aerobic cellular respiration releases energy by using 
oxygen to take metabolize carbohydrates in the cytoplasm and 
mitochondria([link]). Both processes use electron transport chains to 
capture the energy necessary to drive the reactions, because breaking down 
a substance requires energy. These two powerhouse processes, 
photosynthesis and cellular respiration, function in biological, cyclical 
harmony to allow organisms to access life-sustaining energy that originates 
millions of miles away in a burning star humans call the sun. 


Photosynthesis which occurs in the chloroplast consumes 
carbon dioxide and water while producing carbohydrates 
(glucose) and oxygen while Aerobic Cellular respiration 
which occurs in the mitochondria consumes glucose and 
oxygen while producing carbohydrates. (Image by Eva 
Horne and Robert Bear) 


Main Structures and Summary of Photosynthesis 


Photosynthesis requires sunlight, carbon dioxide, and water as starting 
reactants ({link]). After the process is complete, photosynthesis releases 
oxygen and produces carbohydrate molecules, most commonly glucose. 
These sugar molecules contain the energy that living things need to survive. 


Mcarbon dione] 


a 


ech 


- PHOTOSYNTHESIS 


Photosynthesis uses solar energy, 
carbon dioxide, and water to release 
oxygen and to produce energy-storing 
sugar molecules. 


The 


complex reactions of photosynthesis can be summarized by the 


chemical equation shown in [Link]. 


Energy 


Carbon 
Diode + Water + Sunlight Glucose + Oxygen 


The process of photosynthesis can be 
represented by an equation, wherein carbon 
dioxide and water produce sugar and oxygen 

using energy from sunlight. Since the 
products have a higher energy level than the 

reactants, photosynthesis is an endergonic 
reaction. (Image by Robert Bear) 


Although the equation looks simple, the many steps that take place during 
photosynthesis are actually quite complex, as in the way that the reaction 
summarizing cellular respiration represented many individual reactions. 
Before learning the details of how photoautotrophs turn sunlight into food, 
it is important to become familiar with the physical structures involved. 


In plants, photosynthesis takes place primarily in leaves, which consist of 
many layers of cells and have differentiated top and bottom sides. The 
process of photosynthesis occurs not on the surface layers of the leaf, but 
rather in a middle layer called the mesophyll ((link]). The gas exchange of 
carbon dioxide and oxygen occurs through small, regulated openings called 
stomata. 


In all autotrophic eukaryotes, photosynthesis takes place inside an organelle 
called a chloroplast. In plants, chloroplast-containing cells exist in the 
mesophyll. Chloroplasts have a double (inner and outer) membrane. Within 
the chloroplast is a third membrane that forms stacked, disc-shaped 
structures called thylakoids. Embedded in the thylakoid membrane are 
molecules of chlorophyll, a pigment (a molecule that absorbs light) 
through which the entire process of photosynthesis begins. Chlorophyll is 
responsible for the green color of plants. The thylakoid membrane encloses 
an internal space called the thylakoid space. Other types of pigments exist 
that can carry out photosynthesis, but chlorophyll is by far the most 
common. As shown in [link], a stack of thylakoids is called granum, and 
the space surrounding the granum is called stroma (not to be confused with 
stomata, the openings on the leaves). 


Upper 
epidermis 


Mesophyll 


Stomata 7 


Chloroplast 


Outer 
membrane 


J 
IN 7 hylakoids 
Stroma 


Not all cells of a leaf carry out 
photosynthesis. Cells within the 
middle layer of a leaf have 
chloroplasts, which contain the 
photosynthetic apparatus. (credit 
"leaf": modification of work by Cory 
Zanker) 


The Two Parts of Photosynthesis 


Photosynthesis takes place in two stages: the light-dependent reactions and 
the Calvin cycle ({link]). In the light-dependent reactions, which take 
place at the thylakoid membrane, chlorophyll absorbs energy from sunlight 


and then converts it into chemical energy with the use of water. The light- 
dependent reactions release oxygen from the hydrolysis of water as a 
byproduct. In the Calvin cycle, which takes place in the stroma, the 
chemical energy derived from the light-dependent reactions drives both the 
capture of carbon in carbon dioxide molecules and the subsequent assembly 
of sugar molecules. The two reactions use carrier molecules to transport the 
energy from one to the other. The carriers that move energy from the light- 
dependent reactions to the Calvin cycle reactions can be thought of as “full” 
because they bring energy. After the energy is released, the “empty” energy 
carriers return to the light-dependent reactions to obtain more energy. 


The process of photosynthesis is divided to two stages that are linked 
by the energy and electron carriers ATP and NADPH. (Image by Eva 
Horne and Robert Bear) 


The Light-Dependent Reactions 


Introduction 
"And God said, Let there be light: and there was light." The Book of 
Genesis 1:3 


It is interesting that light is one of the first things mentioned in the Bible, 
since light indeed has to be present before any of the other creatures, plant 
or animal, become possible. The light from the sun powers every cell on the 
planet, allowing plants to make food that the rest of us can also partake of. 
How can light be used to make food? When a person turns on a lamp, 
electrical energy becomes light energy. Like all other forms of kinetic 
energy, light can travel, change form, and be harnessed to do work. In the 
case of photosynthesis, light energy is converted into chemical energy, 
which photoautotrophs use to build carbohydrate molecules ({link]). 
However, autotrophs only use a few specific components of sunlight. 


Photoautotrophs can capture 
light energy from the sun, 
converting it into the chemical 
energy used to build food 


molecules. (credit: Gerry 
Atwell) 


What Is Light Energy? 


The sun emits an enormous amount of electromagnetic radiation (solar 
energy). Humans can see only a fraction of this energy, which portion is 
therefore referred to as “visible light.” The manner in which solar energy 
travels is described as waves. Scientists can determine the amount of energy 
of a wave by measuring its wavelength, the distance between consecutive 
points of a wave. A single wave is measured from two consecutive points, 
such as from crest to crest or from trough to trough ([link]). 


Energy Wave 
Wavelength 


The wavelength of a single wave 
is the distance between two 
consecutive points of similar 
position (two crests or two 
troughs) along the wave. 


Visible light constitutes only one of many types of electromagnetic 
radiation emitted from the sun and other stars. Scientists differentiate the 


various types of radiant energy from the sun within the electromagnetic 
spectrum. The electromagnetic spectrum is the range of all possible 
frequencies of radiation ({link]). The difference between wavelengths 
relates to the amount of energy carried by them. 


Green Yellow Orange Red 


GAMMA RAYS X-RAYS UV [VISIBLET INFRARED 


WAVELENGTH 


The sun emits energy in the form of electromagnetic radiation. This 
radiation exists at different wavelengths, each of which has its own 
characteristic energy. All electromagnetic radiation, including visible 
light, is characterized by its wavelength. 


Each type of electromagnetic radiation travels at a particular wavelength. 
The longer the wavelength (or the more stretched out it appears in the 
diagram), the less energy is carried. Short, tight waves carry the most 
energy. This may seem illogical, but think of it in terms of a piece of 
moving a heavy rope. It takes little effort by a person to move a rope in 
long, wide waves. To make a rope move in short, tight waves, a person 
would need to apply significantly more energy. 


The electromagnetic spectrum ([link]) shows several types of 
electromagnetic radiation originating from the sun, including X-rays and 


ultraviolet (UV) rays. The higher-energy waves can penetrate tissues and 
damage cells and DNA, explaining why both X-rays and UV rays can be 
harmful to living organisms. 


Absorption of Light 


Light energy initiates the process of photosynthesis when pigments absorb 
the light. Organic pigments, whether in the human retina or the chloroplast 
thylakoid, have a narrow range of energy levels that they can absorb. 
Energy levels lower than those represented by red light are insufficient to 
raise an orbital electron to a populatable, excited (quantum) state. Energy 
levels higher than those in blue light will physically tear the molecules 
apart, called bleaching. So retinal pigments can only “see” (absorb) 700 nm 
to 400 nm light, which is therefore called visible light. For the same 
reasons, plants pigment molecules absorb only light in the wavelength 
range of 700 nm to 400 nm; plant physiologists refer to this range for plants 
as photosynthetically active radiation. 


The visible light seen by humans as white light actually exists in a rainbow 
of colors. Certain objects, such as a prism or a drop of water, disperse white 
light to reveal the colors to the human eye. The visible light portion of the 
electromagnetic spectrum shows the rainbow of colors, with violet and blue 
having shorter wavelengths, and therefore higher energy. At the other end 
of the spectrum toward red, the wavelengths are longer and have lower 
energy ([link]). 


Longer wavelength 


vewow \/\S\/\/\S 


aw AV AU AC AVAU AC 


AV AC AVAVAUAUAUA 
VIOLET FAVAVAVAVAVAVAVAVAVAT Shorter wavelength 


More energy 


Less energy 


The colors of visible light do not carry the same amount of energy. 
Violet has the shortest wavelength and therefore carries the most 
energy, whereas red has the longest wavelength and carries the least 
amount of energy. (credit: modification of work by NASA) 


Understanding Pigments 


Different kinds of pigments exist, and each has evolved to absorb only 
certain wavelengths (colors) of visible light. Pigments reflect or transmit the 
wavelengths they cannot absorb, making them appear in the corresponding 
color. 


Chlorophylls and carotenoids are the two major classes of photosynthetic 
pigments found in plants and algae; each class has multiple types of 
pigment molecules. There are five major chlorophylls: a, b, c and d anda 
related molecule found in prokaryotes called bacteriochlorophyll. 
Chlorophyll a and chlorophyll b are found in higher plant chloroplasts and 
will be the focus of the following discussion. 


With dozens of different forms, carotenoids are a much larger group of 
pigments. The carotenoids found in fruit—such as the red of tomato 
(lycopene), the yellow of corn seeds (zeaxanthin), or the orange of an 
orange peel ((-carotene)—are used as advertisements to attract seed 
dispersers. In photosynthesis, carotenoids function as photosynthetic 
pigments that are very efficient molecules for the disposal of excess energy. 
When a leaf is exposed to full sun, the light-dependent reactions are 
required to process an enormous amount of energy; if that energy is not 
handled properly, it can do significant damage. Therefore, many carotenoids 
reside in the thylakoid membrane, absorb excess energy, and safely 
dissipate that energy as heat. 


Each type of pigment can be identified by the specific pattern of 
wavelengths it absorbs from visible light, which is the absorption spectrum. 
The graph in [link] shows the absorption spectra for chlorophyll a, 
chlorophyll b, and a type of carotenoid pigment called B-carotene (which 
absorbs blue and green light). Notice how each pigment has a distinct set of 
peaks and troughs, revealing a highly specific pattern of absorption. 
Chlorophyll a absorbs wavelengths from either end of the visible spectrum 
(blue and red), but not green. Because green is reflected or transmitted, 
chlorophyll appears green. Carotenoids absorb in the short-wavelength blue 
region, and reflect the longer yellow, red, and orange wavelengths. 


Absorption Spectra 


Tet ae 


Absorption of light 
inn even SO ne 


- 


: & 
1 
See Se CONN Oaw~ 350 400 450 500 550 600 650 


Wavelength (nm) 
(c) 


(a) Chlorophyll a, (b) chlorophyll b, and (c) B-carotene are 
hydrophobic organic pigments found in the thylakoid 
membrane. Chlorophyll a and b, which are identical except for 
the part indicated in the red box, are responsible for the green 
color of leaves. B-carotene is responsible for the orange color 
in carrots. Each pigment has (d) a unique absorbance spectrum. 


Many photosynthetic organisms have a mixture of pigments; using them, 
the organism can absorb energy from a wider range of wavelengths. Not all 
photosynthetic organisms have full access to sunlight. Some organisms 
grow underwater where light intensity and quality decrease and change with 
depth. Other organisms grow in competition for light. Plants on the 
rainforest floor must be able to absorb any bit of light that comes through, 


because the taller trees absorb most of the sunlight and scatter the 
remaining solar radiation ([link]). 


Plants that commonly grow in the shade 
have adapted to low levels of light by 
changing the relative concentrations of 
their chlorophyll pigments. (credit: Jason 
Hollinger) 


When studying a photosynthetic organism, scientists can determine the 
types of pigments present by generating absorption spectra. An instrument 
called a spectrophotometer can differentiate which wavelengths of light a 
substance can absorb. Spectrophotometers measure transmitted light and 
compute from it the absorption. By extracting pigments from leaves and 
placing these samples into a spectrophotometer, scientists can identify 
which wavelengths of light an organism can absorb. Additional methods for 
the identification of plant pigments include various types of 
chromatography that separate the pigments by their relative affinities to 
solid and mobile phases. 


How Light-Dependent Reactions Work 


The overall function of light-dependent reactions is to convert solar energy 
into chemical energy in the form of NADPH and ATP. This chemical 
energy supports the Calvin cycle and fuels the assembly of sugar molecules. 


The light-dependent reactions are depicted in [link]. Protein complexes and 
pigment molecules work together to produce NADPH and ATP. 


(a) Photosystem II (P680) 


Stroma 

; Reaction Primary Light 
Pigment center electron 
molecules acceptor 


Thylakoid 
membrane 


(b) Photosystem | (P700) 


Light 


A photosystem consists of a light- 
harvesting complex and a reaction 
center. Pigments in the light- 
harvesting complex pass light 
energy to two special chlorophyll 
a molecules in the reaction center. 
The light excites an electron from 
the chlorophyll a pair, which 
passes to the primary electron 


acceptor. The excited electron 
must then be replaced. In (a) 
photosystem II, the electron comes 
from the splitting of water, which 
releases oxygen as a waste 
product. In (b) photosystem I, the 
electron comes from the 
chloroplast electron transport 
chain discussed below. 


The actual step that converts light energy into chemical energy takes place 
in a multiprotein complex called a photosystem [link], two types of which 
are found embedded in the thylakoid membrane, photosystem IT (PSII) and 
photosystem I (PSI) ((link]). The two complexes differ on the basis of what 
they oxidize (that is, the source of the low-energy electron supply) and what 
they reduce (the place to which they deliver their energized electrons). 


Both photosystems have the same basic structure; a number of antenna 
proteins to which the chlorophyll molecules are bound surround the 
reaction center where the photochemistry takes place. Each photosystem is 
serviced by the light-harvesting complex, which passes energy from 
sunlight to the reaction center; it consists of multiple antenna proteins that 
contain a mixture of 300—400 chlorophyll a and b molecules as well as 
other pigments like carotenoids. The absorption of a single photon or 
distinct quantity or “packet” of light by any of the chlorophylls pushes that 
molecule into an excited state. In short, the light energy has now been 
captured by biological molecules but is not stored in any useful form yet. 
The energy is transferred from chlorophyll to chlorophyll until eventually 
(after about a millionth of a second), it is delivered to the reaction center. 
Up to this point, only energy has been transferred between molecules, not 
electrons. 


Electron 
Stroma transport chain 


Light "y+ yt Light 


NADP*+H* NADPH 


In the photosystem II (PSII) reaction center, 
energy from sunlight is used to extract electrons 
from water. The electrons travel through the 
chloroplast electron transport chain to 
photosystem I (PSI), which reduces NADP" to 
NADPH. The electron transport chain moves 
protons across the thylakoid membrane into the 
lumen. At the same time, splitting of water adds 
protons to the lumen, and reduction of NADPH 
removes protons from the stroma. The net result is 
a low pH in the thylakoid lumen, and a high pH in 
the stroma. ATP synthase uses this 
electrochemical gradient to make ATP. 


The reaction center contains a pair of chlorophyll a molecules with a 
special property. Those two chlorophylls can undergo oxidation upon 
excitation; they can actually give up an electron in a process called a 
photoact. It is at this step in the reaction center, this step in photosynthesis, 
that light energy is converted into an excited electron. All of the subsequent 


steps involve getting that electron onto the electron carrier NADP* for 
delivery to the Calvin cycle where the electron is deposited onto carbon for 
long-term storage in the form of a carbohydrate. PSII and PSI are two major 
components of the photosynthetic electron transport chain, which also 
includes the cytochrome complex, a group of reversibly oxidizable and 
reducible proteins that forms part of the electron transport chain between 
PSII and PSI. 


The reaction center of PSII (called P680) delivers its high-energy electrons, 
one at a time, to a Series of proteins and electron carriers (or primary 
electron acceptors, which are pigments or other organic molecules in the 
reaction center that accept energized electrons from the reaction center) that 
sits between it and PSI. P680’s missing electron is replaced by extracting a 
low-energy electron from water; thus, water is split and PSII is re-reduced 
after every photoact. Splitting one HO molecule releases two electrons, 
two hydrogen atoms, and one atom of oxygen. Splitting two molecules is 
required to form one molecule of diatomic O, gas. About 10 percent of the 
oxygen is used by mitochondria in the leaf to support oxidative 
phosphorylation. The remainder escapes to the atmosphere where it is used 
by aerobic organisms to support respiration. 


As electrons move through the proteins that reside between PSII and PSI, 
they lose energy. That energy is used to move hydrogen atoms from the 
stromal side of the membrane to the thylakoid lumen. Those hydrogen 
atoms, plus the ones produced by splitting water, accumulate in the 
thylakoid lumen and will be used synthesize ATP in a later step. Because 
the electrons have lost energy prior to their arrival at PSI, they must be re- 
energized by PSI, hence, another photon is absorbed by the PSI antenna. 
That energy is relayed to the PSI reaction center (called P700). P700 is 
oxidized and sends a high-energy electron to NADP" to form NADPH. 
Thus, PSII captures the energy to make ATP, and PSI captures the energy to 
reduce NADP” into NADPH. The two photosystems work in concert, in 
part, to guarantee that the production of NADPH will roughly equal the 
production of ATP. Other mechanisms exist to fine tune that ratio to exactly 
match the chloroplast’s constantly changing energy needs. 


Generating an Energy Carrier: ATP 


Chemiosmosis 


In chemiosmosis, the free energy from the series of redox reactions just 
described is used to pump hydrogen ions (protons) across the membrane. 
The uneven distribution of H* ions across the thylakoid membrane 
establishes both concentration and electrical gradients (thus, an 
electrochemical gradient), owing to the hydrogen ions’ positive charge and 
their aggregation on one side of the membrane. 


If the thylakoid membrane were open to diffusion by the hydrogen ions, the 
ions would tend to diffuse back across into the matrix, driven by their 
electrochemical gradient. Recall that many ions cannot diffuse through the 
nonpolar regions of phospholipid membranes without the aid of ion 
channels. Similarly, hydrogen ions in the thylakoid lumen can only pass 
through the thylakoid membrane through an integral membrane protein 
called ATP synthase ([link]). This complex protein acts as a tiny generator, 
turned by the force of the hydrogen ions diffusing through it, down their 
electrochemical gradient. The turning parts of this molecular machine 
facilitates the addition of a phosphate to ADP, forming ATP, using the 
potential energy of the hydrogen ion gradient. 


Thylakeid 
Membrane 


Stroma 


ATP synthase is a complex, 
molecular machine that uses a 
proton (H*) gradient to form ATP 
from ADP and inorganic 
phosphate (Pi). (Credit: 
modification of work by Klaus 
Hoffmeier) 


As a review, the buildup of hydrogen ions inside the thylakoid lumen 
creates a concentration gradient. The passive diffusion of hydrogen ions 
from high concentration (in the thylakoid lumen) to low concentration (in 
the stroma) is harnessed to create ATP. The ions build up energy because of 
diffusion and because they all have the same electrical charge, repelling 
each other. To release this energy, hydrogen ions will rush through any 
opening, similar to water jetting through a hole in a dam. In the thylakoid, 
that opening is a passage through a specialized protein channel called the 
ATP synthase. The energy released by the hydrogen ion stream allows ATP 


synthase to attach a third phosphate group to ADP, which forms a molecule 
of ATP ({link]). The flow of hydrogen ions through ATP synthase is called 
chemiosmosis because the ions move from an area of high to an area of low 
concentration through a semi-permeable structure. 


Overview of Light-Dependent Reaction 


Light energy is harvested and transformed into short term chemical energy 
during the light-dependent reactions. The pigments in the reaction center of 
photosytem II absorb light energy and excite electrons into the electron 
transport chain. To replace the electrons excited in photosystem II, water is 
spilt releasing electrons, H* ions and oxygen gas. As the electrons move 
through the electron transport chain, energy, release by the movement of 
electrons, is used to produce a H" ion gradient inside the thylakoid. The 
process of chemiosmosis uses the H* concentration to produce ATP. After 
flowing through the electron transport chain, the electrons enter 
photosystem I. The reaction center of photosystem I absorbs more light 
energy and excites electrons. These energized electrons reduce NADP” to 
NADPH. See ([link])below for a visual representation of the light- 
dependent reactions. 


Light-Dependent 
Reactions 


Thylakoid 
membrane 


This is an image of the Light-Dependent Reactions of photosynthesis. 
(Image by Eva Horne and Robert Bear) 


Calvin Cycle 


"By blending water and minerals from below with sunlight and CO, from 
above, green plants link the earth to the sky. We tend to believe that plants 
grow out of the soil, but in fact most of their substance comes from the air." 
Fritjof Capra, The Web of Life: A New Scientific Understanding of Living 
Systems, (1997) 


After the energy from the sun is converted into chemical energy and 
temporarily stored in ATP and NADPH molecules, the cell has the fuel 
needed to build carbohydrate molecules for long-term energy storage. The 
products of the light-dependent reactions, ATP and NADPH, have lifespans 
in the range of millionths of seconds, whereas the products of the light- 
independent reactions (carbohydrates and other forms of reduced carbon) 
can survive for hundreds of millions of years. Carbohydrates, like the 
cellulose that makes up the bulk of most plants, obviously contain carbon. 
Where does the carbon come from? It comes from the air, in the form of 
carbon dioxide, the gas that is a waste product of respiration in microbes, 
fungi, plants, and animals. 


The Calvin Cycle 


In plants, carbon dioxide (CO>) enters the leaves through stomata, where it 
diffuses over short distances through intercellular spaces until it reaches the 
mesophyll cells. Once in the mesophyll cells, CO> diffuses into the stroma 
of the chloroplast—the site of light-independent reactions of 
photosynthesis. These reactions actually have several names associated with 
them. Another term, the Calvin cycle, is named for the man who discovered 
it, and because these reactions function as a cycle. Others call it the Calvin- 
Benson cycle to include the name of another scientist involved in its 
discovery. The most outdated name is dark reactions (the term originally 
used by Melvin Calvin, who got the Nobel Prize for elucidating these 
reactions), because light is not directly required ([link]). However, the term 
dark reactions can be misleading because it implies incorrectly that the 
reaction only occurs at night or is independent of light, which is why it has 
faded from everyday usage. 


Chloroplast 


Light reactions harness energy from the sun to produce 
chemical bonds, ATP, and NADPH. These energy-carrying 
molecules are made in the stroma where carbon fixation takes 
place. Work by Eva Horne and Robert A. Bear 


The light-independent reactions of the Calvin cycle can be organized into 
three basic stages: fixation, reduction, and regeneration. 


Stage 1: Fixation 


In the stroma, in addition to CO», two other components are present to 
initiate the light-independent reactions: an enzyme called ribulose 
bisphosphate carboxylase (RuBisCO), and three molecules of ribulose 
bisphosphate (RuUBP), as shown in [link]. RuBP has five atoms of carbon, 
flanked by two phosphates. 


1/2 molecule glucose (CgH;20¢) 


The Calvin cycle has three stages. In stage 1, the 
enzyme RuBisCO incorporates carbon dioxide into 
an organic molecule, PGA. In stage 2, the organic 
molecule is reduced using electrons supplied by 
NADPH. In stage 3, RuBP, the molecule that starts 
the cycle, is regenerated so that the cycle can 
continue. Only one carbon dioxide molecule is 
incorporated at a time, so the cycle must be 
completed three times to produce a single three- 
carbon PGAL molecule, and six times to produce a 
six-carbon glucose molecule. (Original by 
OpenStax Modified by Robert A. Bear) 


RuBisCO catalyzes a reaction between CO» and RuBP. For each CO» 
molecule that reacts with one RuBP, two molecules of phosphoglycerate 
(PGA) form. PGA has three carbons and one phosphate. Each turn of the 
cycle involves only one RuBP and one carbon dioxide and forms two 


molecules of PGA. The number of carbon atoms remains the same, as the 
atoms move to form new bonds during the reactions (3 atoms from 3CO, + 
15 atoms from 3RuBP = 18 atoms in 3 atoms of PGA). This process is 
called carbon fixation, because CO, is “fixed” from an inorganic form into 
organic molecules. 


Stage 2: Reduction 


ATP and NADPH are used to convert the six molecules of PGA into six 
molecules of a chemical called phosphoglyceraldehyde (PGAL). That is a 
reduction reaction because it involves the gain of electrons (from NADPH) 
by PGA. Recall that a reduction is the gain of an electron by an atom or 
molecule. Six molecules of both ATP and NADPH are used; making 
glucose is obviously an energy-intensive activity. For ATP, energy is 
released with the loss of the terminal phosphate atom, converting it into 
ADP; for NADPH, both energy and a hydrogen atom are lost, converting it 
into NADP". Both of these molecules return to the nearby site of the light- 
dependent reactions to be reused and re-energized. 


Stage 3: Regeneration 


Interestingly, at this point, only one of the PGAL molecules leaves the 
Calvin cycle and is sent to the cytoplasm to contribute to the formation of 
other compounds needed by the plant. Because the PGAL exported from 
the chloroplast has three carbon atoms, it takes three “turns” of the Calvin 
cycle to fix enough net carbon to export one PGAL. But each turn makes 
two PGAL, thus three turns make six PGAL. One is exported while the 
remaining five PGAL molecules remain in the cycle and are used to 
regenerate RuBP, which enables the system to prepare for more CO, to be 
fixed. Three more molecules of ATP are used in these regeneration 
reactions. 


Overview of Calvin Cycle 


During the Calvin cycle, energy and electrons harvested in the light- 
dependent reactions are used to produce carbohydrates i.e. glucose. There 
are three stages in the Calvin cycle. The first stage is carbon fixation, CO 
from the atmosphere is attached to an organic molecule RuBP during this 
stage. The second stage is the carbon reduction, the energy and electrons in 
ATP and NADPH are used to produce carbohydrates (glucose). The last 
Stage is the regeneration stage, energy from ATP is used to regenerate the 
first substrate of the cycle (RUBP). See ({link]) below for a review of the 
Calvin Cycle. 


Calvin Cycle — 


This image represents the Calvin Cycle. (Image by Eva Home and 
Robert Bear) 


Note: 

Evolution Connection 

Photosynthesis 

During the evolution of photosynthesis, a major shift occurred from the 
bacterial type of photosynthesis that involves only one photosystem and is 
typically anoxygenic (does not generate oxygen) into modern oxygenic 
(does generate oxygen) photosynthesis, employing two photosystems. This 
modern oxygenic photosynthesis is used by many organisms—from giant 
tropical leaves in the rainforest to tiny cyanobacterial cells—and the 
process and components of this photosynthesis remain largely the same. 
Photosystems absorb light and use electron transport chains to convert 
energy into the chemical energy of ATP and NADH. The subsequent light- 
independent reactions then assemble carbohydrate molecules with this 
energy. 

Photosynthesis in desert plants has evolved adaptations that conserve 
water. In the harsh dry heat, every drop of water must be used to survive. 
Because stomata must open to allow for the uptake of CO>, water escapes 
from the leaf during active photosynthesis. Desert plants have evolved 
processes to conserve water and deal with harsh conditions. A more 
efficient use of CO> allows plants to adapt to living with less water. Some 
plants such as cacti ({link]) can prepare materials for photosynthesis during 
the night by a temporary carbon fixation/storage process, because opening 
the stomata at this time conserves water due to cooler temperatures. In 
addition, cacti have evolved the ability to carry out low levels of 
photosynthesis without opening stomata at all, an extreme mechanism to 
face extremely dry periods. 


The harsh conditions of the desert have led plants 
like these cacti to evolve variations of the light- 
independent reactions of photosynthesis. These 

variations increase the efficiency of water usage, 

helping to conserve water and energy. (credit: 
David A. Rintoul) 


Overview of Photosynthesis 


Photosynthesis converts light energy to chemical energy in two stages, the 
light-dependent reactions and the Calvin cycle. By exploring these two sets 
of reactions, we learned how photons of light energy are turned into food by 
photosynthesis. The light-dependent reactions harvest the light energy to 
make ATP and to transfer electrons from H»O to NADP" forming NADPH 
and Oxygen gas. The energy and electrons in ATP and NADPH are used in 
the Calvin cycle to produce glucose from carbon dioxide. The sunlight 
energy entering the chloroplasts becomes stored as the chemical bonds in 
the organic molecules. See ({link]) below for a review of photosynthesis. 


eed 


The process of photosynthesis is divided to two stages 
that are linked by the energy and electron carriers ATP 
and NADPH. The light-dependent reactions split water 
and releases oxygen as a byproduct, and these reactions 
convert light energy to chemical energy (ATP and 
NADPH). The Calvin cycle uses the energy in ATP and 
NADPH and produces carbohydrates by fixing CO, a 


byproduct of aerobic cellular respiration. (Image by Eva 
Horne and Robert Bear) 


What is the fate of the carbohydrates produced by photosynthesis? About 
50% of the carbohydrates are used by the plant for aerobic cellular 
respiration in their mitochondria. The other 50% of the carbohydrates are 
the building blocks for the biological macromolecules the make up plant 
cells that you learned about in module 3. As you may realize, these 
biological macromolecules are the food we eat, and you are what you eat. 
Taking this a bit further, all the activities you do from reading this text to 
sleeping require energy and that energy comes from the Sun. 


Overview of Cellular Respiration 
This is a general overview of cellular respiration. 


Introduction 

"Surely the mitochondrion that first entered another cell was not thinking 
about the future benefits of cooperation and integration; it was merely 
trying to make its own living in a tough Darwinian world." Stephen Jay 
Gould, in Wonderful Life: the Burgess Shale and the Nature of History, 
(1990) 


All living organisms require energy, and for all organisms this energy 
comes from the chemical energy found in compounds that they acquire 
from their environment. The mitochondrion, a descendent of an aerobically- 
respiring bacteria, is the site of energy generation in eukaryotes. As we 
learned previously, the process of photosynthesis uses solar energy 
(sunlight) and converts this energy into chemical energy in the form of 
carbohydrates. In order for the chemical energy in the carbohydrates to be 
made available to do cellular work, the energy must be converted into a 
useable form known as ATP. Adenosine Triphosphate is the energy currency 
of the cell, and everything you do from walking down the street to reading 
this book requires energy in the form of ATP. Organisms need a constant 
supply of ATP, and the potential energy stored in food is the source of 
energy to meet this need. By connecting all this together, you should realize 
that your daily activities are fueled by the energy from the sun and that even 
on the cellular level nutrients cycle and energy flows ([link]). 


This image illustrates the relationship between 
photosynthesis and cellular respiration. (Image by Eva 
Horne and Robert Bear) 


All organisms need ATP, but not all organisms use the same pathways to 
generate ATP from the food that is consumed. Aerobic cellular 
respiration, the main subject of this chapter, uses oxygen (O>) and glucose 
to generate ATP. Organisms (plants, animals, fungi and microbes) that live 
in an oxygen (O>) rich environment use this process to generate ATP. The 
overall equation for aerobic cellular respiration is the reverse of 
photosynthesis, is an exergonic reaction, and supplies the ATP for cellular 
functions ([Link]). 


Aerobic Cellular Respiration 


Energy 


Carbon 
———————> 
Glucose + Oxygen ATP + Dioxide * Water 


This image illustrates the overall equation for 
aerobic cellular respiration and how the amounts of 
free energy differs between the reactants and the 
products. (Image by Robert Bear) 


As the aerobic cellular respiration equation shows ([link]), an organism 
needs to acquire the O> from its surroundings and to get rid of the CO, that 
is produced. The acquisition of O» and the release of CO, is accomplished 
in a variety of ways. In single celled organisms, the movement of O» and 
CO> (gas exchange) is done by simple diffusion. However, in complex 
organisms there are specialized organs that allow for gas exchange; for 
example, gills in aquatic organisms and lungs in terrestrial animals. 


A common misconception is that plants do not undergo cellular respiration 
because they make their own energy by photosynthesis. Plants do perform 
cellular respiration using the carbohydrates produced via photosynthesis; 
this occurs in tissues that are not photosynthetically active (e.g., roots), as 
well as in leaves and stems. Approximately half of the glucose produced by 
photosynthesis is consumed by the plant, mostly to generate ATP during 
aerobic cellular respiration. Other uses of glucose in the plant include 
synthesis of cell walls, starch, and other plant carbohydrates. So, plants 
harvest light energy via photosynthesis, making carbohydrates, and then 
they use the energy stored in those carbohydrates to perform various 
cellular functions. This is the reason why they are called autotrophs, or self 
feeders. 


Some single-celled organisms use anaerobic metabolism to extract energy 
from biological molecules; this process occurs in the absence of oxygen. In 
this chapter, we will explore one type of anaerobic metabolism called 
fermentation. You may already be familiar with a one type of fermentation, 
lactic acid fermentation, especially if you have recently over-exerted your 
muscles. Anaerobic metabolism is used by many organisms to produce ATP 
when oxygen is not available and thus pathways which require oxygen 
cannot be used. The amount of ATP produced by fermentation is much less 
then that produced by aerobic cellular respiration, so there is a cost and 
benefit associated with organisms utilizing fermentation. 


Summary of Aerobic Cellular Respiration 


Aerobic cellular respiration ([link]) is series of linked chemical reactions 
that can be best understood if it is separated into four stages. These are 
glycolysis, pyruvate oxidation, the Krebs Cycle, and oxidative 
phosphorylation. Similar to photosynthesis, cellular respiration uses a 
series of oxidation-reduction reactions. During these reactions, electrons are 
stripped from the chemical bonds of the original glucose molecule and 
eventually added to oxygen, via a series of intermediate steps. This series of 
reactions releases small amounts of energy at each step; this energy is used 
to drive the formation of ATP. This section is a brief introduction to the 
stages of aerobic respiration with more detail to follow in the chapter. 


Cytoplasm Caos 


ATP 


Oxidative 


Phosphory- 
lation 


Aerobic Cellular Respiration 


This image illustrates aerobic cellular respiration. (Image by Eva 
Horne and Robert Bear) 


The first stage of cellular respiration is called Glycolysis and occurs in the 
cytoplasm of the cell. During glycolysis, 1 glucose molecule (with 6 carbon 
atoms) is broken down into 2 pyruvate molecules (with three carbon atoms 
each). This is accompanied by the production of a few ATP molecules and 
the storage of some high-energy electrons on the electron carrier NADH. 
Note that no O> is needed for this set of reactions, which means that 
glycolysis can proceed in the absence of oxygen. 


The second stage is a short series of reactions called the oxidation of 
pyruvate during which pyruvate (3 carbon atoms) is converted to acetyl- 
CoA (two carbon atoms), accompanied by the production of CO» (one 


carbon atom). This process occurs on the mitochondrial inner membrane, 
and as a result the acetyl-CoA is formed inside the mitochondria. Pyruvate 
is made in the cytoplasm, and this step moves the next compound in the 
pathway into the mitochodria. This is critical, since all subsequent steps in 
the pathway occur within the mitochondria. The other important event of 
this stage is the addition of high-energy electrons to NAD", generating 
another molecule of the electron carrier NADH. 


Acetyl-CoA enters into the Krebs cycle, a series of mitochondrial reactions 
that completes the breakdown of the original glucose, thereby releasing 
CO>. In this third stage of the process, energy is harvested in the form of 
high-energy electrons being used to generate NADH as well as another 
high-energy electron carrier, FADHp. The reactions of the Krebs cycle also 
produce a small amount of ATP. 


So far, a minimal amount of ATP has been produced, but a lot of energy has 
been stored in the electron carriers NADH and FADH). In the final stage of 
aerobic cellular respiration, Oxidative Phosphorylation, a series of 
enzymes known as the electron transport chain uses those high-energy 
electrons to produce a large amount of ATP. The high energy electrons 
harvested in the first three stages, and ferried by electron carriers (NADH 
and FADH,) to the electron transport chain, are used to produce large 
amounts of ATP vir the mitochondrial membrane protein known as the ATP 
synthase. During this final stage is also when atmospheric oxygen is used 
as the final electron and hydrogen ion acceptor, in a reaction which 
produces water. The need for O> in this final step means that these reactions 
are part of aerobic cellular respiration. 


Location and Structures of Aerobic Cellular Respiration 


All eukaryotic cells (protists, fungi, plants and animals) have mitochondria, 
and mitochondria are often called the power plants of the cell because these 
organelles produce a large amount of ATP. As you may remember from a 
previous module, the mitochondrion is an organelle that is hypothesized to 
have originated as an endosymbiotic aerobic bacteria. Some of the evidence 
for this hypothesis comes from the relationship of the functional parts of the 
mitochondria (({link]) to the structure of a typical aerobic bacteria. There is 


an outer membrane which defines the organelle and represents the 
membrane which enveloped the bacteria when it was taken into the cell via 
endocytosis. The inner membrane represents the plasma membrane of the 
bacteria; the inner and outer membranes together form the intermembrane 
space. The inner membrane is highly folded; these folds are called 
cristae. The extensive folding increases the surface area for the numerous 
electron transport chain enzymes and the ATP synthases that are used to 
make ATP. In bacteria all of these enzymes are packed into the plasma 
membrane, as one would expect if the endosymbiotic hypothesis is correct. 
The production of ATP is driven by a concentration gradient between the 
outer and inner compartment; in aerobic bacteria this concentration gradient 
is between the inside and the outside of the cell. The innermost 
compartment, derived from the cytoplasm of the ancestral bacteria, is called 
the matrix, and this compartment (just like the cytoplasm of today's 
bacteria) contains ribosomes and DNA; It is also the location of the Krebs 
Cycle reactions. 


Intermembrane space Inner Membrane 


HAAN 


Outer Membrane Matrix 


This image illustrates the structures within the mitochondria. (Image 


by Eva Horne and Robert Bear) 


Glycolysis 


Introduction 

"My main thesis will be that in the study of the intermediate processes of 
metabolism we have to deal not with complex substances which elude 
ordinary chemical methods, but with the simple substances undergoing 
comprehensible reactions." Sir Frederick Gowland Hopkins, 1933 


You have read that nearly all of the energy used by living cells comes to 
them in the bonds of the simple 6-carbon sugar, glucose. Glycolysis 
(literally "sugar splitting") is the first step in the breakdown of glucose to 
extract energy for cellular metabolism. Nearly all living organisms carry out 
glycolysis as part of their metabolism. The process does not use oxygen and 
is therefore anaerobic. Glycolysis takes place in the cytoplasm of both 
prokaryotic and eukaryotic cells. 


Glycolysis begins with the six carbon ring-shaped structure of a single 
glucose molecule and ends with two molecules of a three-carbon sugar 
called pyruvate. Glycolysis consists of two distinct phases. The first part of 
the glycolysis pathway traps the glucose molecule in the cell and uses 
energy to modify it so that the six-carbon sugar molecule can be split 
evenly into the two three-carbon molecules. The second part of glycolysis 
extracts energy from the chemical bonds in the molecules and stores it in 
the form of ATP and NADH, the reduced form of NAD. 


First Half of Glycolysis (Energy-Requiring Steps) 


Step 1. The first step in glycolysis ([link]) is catalyzed by hexokinase, an 
enzyme with broad specificity that catalyzes the phosphorylation (addition 
of a phosphate molecule) of six-carbon sugars. Hexokinase phosphorylates 
glucose using ATP as the source of the phosphate, producing glucose-6- 
phosphate, a more high-energy form of glucose. This reaction prevents the 
phosphorylated glucose molecule from being transported out of the cell via 
glucose transporters in the plasma memrane. It can no longer leave the cell 
because the transport proteins recognize unmodified glucose, but not the 
phosphorylated version. 


Step 2. In the second step of glycolysis, an isomerase converts glucose-6- 
phosphate into one of its isomers, fructose-6-phosphate. An isomerase is an 
enzyme that catalyzes the conversion of a molecule into one of its isomers 
(compounds with the same numbers and kinds of atoms arranged in 
different configurations). This change from phosphoglucose to 
phosphofructose facilitates the eventual split of the sugar into two three- 
carbon molecules. 


Step 3. The third step is the phosphorylation of fructose-6-phosphate, 
catalyzed by the enzyme phosphofructokinase. A second ATP molecule 
donates a high-energy phosphate to fructose-6-phosphate, producing 
fructose-1,6-bisphosphate. In this pathway, phosphofructokinase is a rate- 
limiting enzyme. It is active when the concentration of ADP is high; it is 
less active when ADP levels are low and the concentration of ATP is high. 
Thus, if there is “sufficient” ATP in the system, the pathway slows down. 
This is a type of end product inhibition, since ATP is the end product of 
glucose catabolism. 


Step 4. The newly added high-energy phosphate further destabilizes 
fructose-1,6-bisphosphate, which is now a very high-energy compound. The 
fourth step in glycolysis employs an enzyme, aldolase, to cleave fructose- 
1,6-bisphosphate into two phosphorylated three-carbon isomers: 
dihydroxyacetone-phosphate and glyceraldehyde-3-phosphate. 


Step 5. In the fifth step, an isomerase transforms the dihydroxyacetone- 
phosphate into its isomer, glyceraldehyde-3-phosphate. Thus, the pathway 
will continue with two molecules of a single isomer. At this point in the 
pathway, there is a net investment of energy from two ATP molecules in the 
breakdown of one glucose molecule. 


WY 
@ 2 @ @  f-0-420 
H C20 O 
A H (e) a P 
H H-C=0 H-C-OH He=O=hIO HO-C=H —_ Dihydroxyacetone- 
HeCeOH ATP = ADP -C-OH c2o ATP ADP 414} phosphate 
' ' = 
CH-O HOsC 


H 
H HO-C-H 
H / NY ie oe : en HO-CH Fructose Triose 
Cc Cc i > = en bisphosphate hosphate (5) 
HO” Ne iv Non Hexokinase H-C-OH _ Phosphoglucose Hee _ Phosphofructo- H Cc ‘OH aldose P pipiens 
C=C 1” 9 isomerase 1 9 kinase H=C-OH 07 
' 


H OH H-G-O-Ps0 HG Osea H-¢-0-P=0 " 
H fo H o 4 § 7 ¢=0 
fe asec H=C*OH g- Glyceraldehyde- 
Glucose Glucose-6-phosphate Fructose-6-phosphate Fructose-1,6-biphosphate i ‘ _o-b2o  3-phosphate 
A ¢& 


The first half of glycolysis uses two ATP molecules in the 
phosphorylation of glucose, which is then split into two three-carbon 
molecules. 


Second Half of Glycolysis (Energy-Releasing Steps) 


So far, glycolysis has cost the cell two ATP molecules and produced two 
small, three-carbon sugar molecules. Both of these molecules will proceed 
through the second half of the pathway, and sufficient energy will be 
extracted to pay back the two ATP molecules used as an initial investment 
and produce a profit for the cell of two additional ATP molecules and two 
even higher-energy NADH molecules. 


Step 6. The sixth step in glycolysis ({link]) oxidizes the sugar 
(glyceraldehyde-3-phosphate), extracting high-energy electrons, which are 
picked up by the electron carrier NAD*, producing NADH. The sugar is 
then phosphorylated by the addition of a second phosphate group, 
producing 1,3-bisphosphoglycerate. Note that the addition of a second 
phosphate group does not require another high-energy ATP molecule; 
inorganic phosphate ions in the cytoplasm are used instead. 


0 
yao 
H-C-OHO" Glyceraldehyde- 
H-C-o-P20 ~—- 3-phosphate 
H ¢ 


Glyceraldehyde- NAD* + P; 
3-phosphate ® 
dehydrogenase 
NADH + H* 
2X 


z H.O . 7 “O-P*0 
0. 0 ATP ADP Oy 2 om OQ, 0 ATP ADP ¢ 
° H ¢ -O 3 =O H ¢ x pel 
C=O <= a LO onsen, EOHO H-C-OHO" 
yruvate Cc fe) Enolase H-C-OH 6 Phosphoglycerate H-C-O-P=0 Phosphoglycerate 1 
H°C*H kinase H**H 4 mutase 4 A kinase H-C~ O-P=O 
H H o 
Pyruvate fe a 2-Phosphoglycerate 3-Phosphoglycerate 1,3-Bisphosphoglycerate 


The second half of glycolysis involves phosphorylation without ATP 
investment (step 6) and produces two NADH and four ATP 
molecules per glucose. 


Here again is a potential limiting factor for this pathway. The continuation 
of the reaction depends upon the availability of the oxidized form of the 
electron carrier, NAD*. Thus, NADH must be continuously oxidized back 
into NAD" in order to keep this step going. If NAD* is not available, the 
second half of glycolysis slows down or stops. If oxygen is available in the 
system, the NADH will be oxidized readily, though indirectly, and the high- 
energy electrons from the hydrogen released in this process will be used to 
produce ATP. In an environment without oxygen, an alternate pathway 
(fermentation) can provide the oxidation of NADH to NAD". 


Step 7. In the seventh step, catalyzed by phosphoglycerate kinase (an 
enzyme named for the reverse reaction), 1,3-bisphosphoglycerate donates a 
high-energy phosphate to ADP, forming one molecule of ATP. This is an 
example of substrate-level phosphorylation, where a phosphate group is 
added to ADP by removing it from another compound rather than from the 
phosphate ions in the cytoplasm.. A carbonyl group on the 1,3- 
bisphosphoglycerate is oxidized to a carboxyl group, and 3- 
phosphoglycerate is formed. 


Step 8. In the eighth step, the remaining phosphate group in 3- 
phosphoglycerate moves from the third carbon to the second carbon, 
producing 2-phosphoglycerate (an isomer of 3-phosphoglycerate). The 
enzyme catalyzing this step is a mutase (isomerase). 


Step 9. An enzyme called enolase catalyzes the ninth step. This enzyme 
causes 2-phosphoglycerate to lose water from its structure; this is a 
condensation reaction, resulting in the formation of a double bond that 
increases the potential energy in the remaining phosphate bond and 
produces phosphoenolpyruvate (PEP). 


Step 10. The last step in glycolysis is catalyzed by the enzyme pyruvate 
kinase (the enzyme in this case is named for the reverse reaction of 
pyruvate’s conversion into PEP) and results in the production of a second 
ATP molecule by substrate-level phosphorylation and the compound 
pyruvic acid (or its salt form, pyruvate). Many enzymes in enzymatic 
pathways are named for the reverse reactions, since the enzyme can 
catalyze both forward and reverse reactions (these may have been described 
initially by the reverse reaction that takes place in vitro, under non- 
physiological conditions). 


Outcomes of Glycolysis 


Glycolysis starts with glucose and produces two pyruvate molecules, a total 
of four ATP molecules and two molecules of NADH ([link]). Two ATP 
molecules were used in the first half of the pathway to prepare the six- 
carbon ring for cleavage, so the cell has a net gain of two pyruvate 
molecules, two ATP molecules and 2 NADH molecules for its use. If the 
cell cannot catabolize the pyruvate molecules further, it will harvest only 
these two ATP molecules from one molecule of glucose. For example, 
mature mammalian red blood cells are not capable of aerobic cellular 
respiration (they have no mitochondria), so glycolysis is their sole source of 
ATP. 


Cytoplasm 


Glycolysis 


This image is an overview of glycolysis which occurs in the 
cytoplasm of a cell. Glucose is catabolized into 2 pyruvate molecules 
with 2 NAD* reduced to 2 NADH. Two ATP molecules are 
consumed, while 4 are produced, yielding a net gain of 2 ATP 
molecules. (Image by Eva Horne and Robert Bear 


Oxidation of Pyruvate and the Krebs Cycle 


"It is the destiny of wine to be drunk, and it is the destiny of glucose to be 
oxidized. But it was not oxidized immediately: its drinker kept it in his liver 
for more than a week, well curled up and tranquil, as a reserve aliment for a 
sudden effort; an effort that he was forced to make the following Sunday, 
pursuing a bolting horse. " Primo Levi, The Periodic Table, 1975 


If oxygen is available, aerobic cellular respiration will go forward. In 
eukaryotic cells, the pyruvate molecules produced at the end of glycolysis 
are transported into mitochondria, which are the sites of aerobic cellular 
respiration. There, pyruvate (three carbons) will be transformed into an 
acetyl group (two carbons) that will be attached to a carrier compound 
called coenzyme A (CoA). The resulting compound is called acetyl-CoA. 
CoA is made from vitamin B5, pantothenic acid. Acetyl-CoA can be used 
in a variety of ways by the cell, but its major function is to deliver the two- 
carbon energy source derived from pyruvate to the next stage of the aerobic 
cellular respiration pathway. 


Oxidation of Pyruvate 


In order for pyruvate, the product of glycolysis, to enter the next pathway, it 
must undergo several changes. The conversion is a three-step process 
({link]). 


Oxidation of Pyruvate 


NAD* NADH 
ae 
COE 


Oxidation 
reaction 


A carboxyl group NAD* is reduced An acetyl group is 

is removed from to NADH. transferred to 

pyruvate, releasing coenzyme A, 

carbon dioxide. resulting in acetyl - 
CoA. 


Upon entering the mitochondrial 
matrix, a multi-enzyme complex 
converts pyruvate into acetyl-CoA. In 
the process, carbon dioxide is released 
and one molecule of NADH is 
formed. 


Step 1. A carboxyl group is removed from pyruvate, releasing a molecule of 
carbon dioxide into the surrounding medium. The result of this step is a 
two-carbon hydroxyethyl group bound to the enzyme (pyruvate 
dehydrogenase). This is the first of the six carbons from the original glucose 
molecule to be removed. This step proceeds twice for each glucose 
molecule (remember: there are two pyruvate molecules produced at the end 
of glycolsis). Thus, two of the six carbons will have been removed at the 
end of this step in aerobic cellular respiration. 


Step 2. The hydroxyethyl group is oxidized to an acetyl group, and the 
electrons are picked up by NAD”, forming NADH. The high-energy 
electrons from NADH will be used later to generate ATP. 


Step 3. The enzyme-bound acetyl group is transferred to CoA, producing a 
molecule of acetyl-CoA. 


During the oxidation of pyruvate, the incoming pyruvate is converted to 
acetyl-CoA, NAD” is reduced to NADH and a carbon dioxide is released 
for each pyruvate entering the stage ([Link]). 


Cytoplasm Cinco 
v 


Oxidation of Pyruvate 


This image is an overview of the oxidation of pyruvate. During this 
stage, carbon dioxide is release, NAD™ is reduced to NADH and 
acetyl-CoA is formed. (Image by Eva Horne and Robert Bear) 


Krebs Cycle 


In the presence of oxygen, the two carbons in acetyl-CoA are added to to a 
four-carbon molecule, oxaloacetate, to form citrate (aka citric acid), a six- 
carbon molecule. This is the starting point of the Krebs Cycle, which will 
harvest the remainder of the extractable energy from what began as a 
glucose molecule. This single pathway has several different names: the 
citric acid cycle (for citric acid, the first compound in the cycle), the 
tricarboxylic acid (TCA) cycle (since citric acid has 3 carboxyl groups, and 
is thus a tricarboxylic acids), and the Krebs cycle, after Hans Krebs, who 
first identified the steps in the pathway in the 1930s in pigeon flight 
muscles. This work earned Krebs a share (with Fritz Lippman) of the 1953 
Nobel Prize in Physiology and Medicine. 


After the conversion of pyruvate to acetyl CoA by enzymes in the 
mitochondrial inner membrane, the Krebs cycle takes place in the matrix of 
mitochondria. Almost all of the enzymes of the Krebs cycle are soluble 
(i.e., not bound to the membrane), with the single exception of the enzyme 
succinate dehydrogenase, which is embedded in the inner membrane of the 
mitochondrion. Unlike glycolysis, the Krebs cycle is a closed loop: The last 
part of the pathway regenerates the compound (oxaloacetate) used in the 
first step. The eight steps of the cycle are a series of redox, condensation, 
hydrolysis, and decarboxylation reactions that produce two carbon dioxide 
molecules, one GTP/ATP, and reduced forms of NADH and FADH> 
({link]). Even though oxygen is not directly required for these reactions, this 
is considered an aerobic pathway because the NADH and FADH) produced 
must transfer their electrons to the next pathway in the system, which will 
use oxygen. If this transfer does not occur, there won't be any NAD or 
FADH regenerated, and the oxidation steps of the Krebs cycle cannot occur 
without those oxidized electron carriers. Note that the Krebs cycle produces 
very little ATP directly and does not directly consume oxygen. 


QO CoA 
| ie 
ees | 
: CH2 
COoo™ | | 
| HO —C —COO™ 
o=C | C2 | | 
| . Acetyl CoA on 
a \ | coo" 
ie \ H,0 COoOo™ 
ae |__coo" | \ SH-CoA CH2 
nO " NADH/H* | Cg CE HC — COO- 
Z F | 
a NAD Oxaloacetate cere. | : HO — cH 
| — 
COOs = 
Ca Isocitrate COO 
Malate NAD* 
Ccoo™ J NADH/H* 
H,0 Se JOO: 
CH a Cs al 
Il 4 
HC a-Ketoglutarate CH 
| Fumarate NAD* | 
COO- SH-CoA CH> 
aa Cc NADH/H* | 
ee a cS) ae i iia 
[FAD] Succinate sia das 
/ COO- 
aH, / 7 SN \ 
/ ctp Pt CoOo™ 
vs SH-CoA GDP 
COO- CH2 
| | 
CH2 CH2 
| | 
iis aes 
COO- S—CoA 


In the Krebs cycle, the acetyl group from acetyl CoA is 
attached to a four-carbon oxaloacetate molecule to form 
a six-carbon citrate molecule. Through a series of steps, 
citrate is oxidized, releasing two carbon dioxide 
molecules for each acetyl group fed into the cycle. In the 
process, three NAD* molecules are reduced to NADH, 
one FAD molecule is reduced to FADH, and one ATP or 
GTP (depending on the cell type) is produced (by 
substrate-level phosphorylation). Because the final 
product of the citric acid cycle is also the first reactant, 
the cycle runs continuously in the presence of sufficient 


reactants. (credit: modification of work by 
“Yikrazuul”/Wikimedia Commons) 


Steps in the Krebs Cycle 


Step 1. Prior to the start of the first step, a transitional phase occurs during 
which pyruvic acid is converted to acetyl-CoA. Then, the first step of the 
cycle begins: This is a condensation step, combining the two-carbon acetyl 
group with a four-carbon oxaloacetate molecule to form a six-carbon 
molecule of citrate. CoA is bound to a sulfhydryl group (-SH) and diffuses 
away to eventually combine with another acetyl group. This step is 
irreversible because it is highly exergonic. The rate of this reaction is 
controlled by negative feedback and the amount of ATP available. If ATP 
levels increase, the rate of this reaction decreases. If ATP is in short supply, 
the rate increases. 


Step 2. In step two, citrate loses one water molecule and gains another as 
citrate is converted into its isomer, isocitrate. 


Step 3. In step three, isocitrate is oxidized, producing a five-carbon 
molecule, a-ketoglutarate, together with a molecule of CO, and two 
electrons, which reduce NAD* to NADH. This step is also regulated by 
negative feedback from ATP and NADH, and a positive effect of ADP. 


Steps 3 and 4. Steps three and four are both oxidation and decarboxylation 
steps, which release electrons that reduce NAD* to NADH and release 
carboxyl groups that form CO, molecules. a-Ketoglutarate is the product of 
step three, and a succinyl group is the product of step four. CoA binds the 
succinyl group to form succinyl CoA. The enzyme that catalyzes step four 
is regulated by feedback inhibition of ATP, succinyl CoA, and NADH. 


Step 5. In step five, a phosphate group is substituted for coenzyme A, and a 
high-energy bond is formed. This energy is used in substrate-level 
phosphorylation (during the conversion of the succinyl group to succinate) 
to form either guanine triphosphate (GTP) or ATP. There are two forms of 


the enzyme, called isoenzymes, for this step, depending upon the type of 
animal tissue in which they are found. One form is found in tissues that use 
large amounts of ATP, such as heart and skeletal muscle. This form 
produces ATP. The second form of the enzyme is found in tissues that have 
a high number of anabolic pathways, such as liver. This form produces 
GTP. GTP is energetically equivalent to ATP; however, its use is more 
restricted. In particular, protein synthesis primarily uses GTP. 


Step 6. Step six is a condensation reaction that converts succinate into 
fumarate. Two hydrogen atoms are transferred to FAD, producing FADH). 
The energy contained in the electrons of these atoms is insufficient to 
reduce NAD* but adequate to reduce FAD. Unlike NADH, this carrier 
remains attached to the enzyme and transfers the electrons to the electron 
transport chain directly. This process is made possible by the localization of 
the enzyme catalyzing this step inside the inner membrane of the 
mitochondrion. 


Step 7. Water is added to fumarate during step seven, and malate is 
produced. The last step in the Krebs cycle regenerates oxaloacetate by 
oxidizing malate. Another molecule of NADH is produced in the process. 


Products of the Krebs Cycle 


Two carbon atoms come into the Krebs cycle from each acetyl group, 
representing four out of the six carbons of one glucose molecule. Two 
carbon dioxide molecules are released on each turn of the cycle; however, 
these do not necessarily contain the most recently added carbon atoms. The 
two acetyl carbon atoms will eventually be released on later turns of the 
cycle; thus, all six carbon atoms from the original glucose molecule are 
eventually incorporated into carbon dioxide. Each turn of the cycle forms 
three NADH molecules and one FADH> molecule. These carriers will 
connect with the last portion of aerobic respiration to produce ATP 
molecules. One ATP is also made in each cycle ([link]). 


Glucose 


Cytoplasm 
V ATP. 


Pyruvate 


Acetyl-CoA 


Krebs Cycle 


This is an overview of the Krebs cycle. (Image by Eva Horne and 
Robert Bear) 


Oxidative Phosphorylation 


Introduction 

"Finally, to the theme of the respiratory chain, it is especially noteworthy 
that David Keilin's chemically simple view of the respiratory chain appears 
now to have been right all along — and he deserves great credit for having 
been so reluctant to become involved when the energy-rich chemical 
intermediates began to be so fashionable. This reminds me of the aphorism: 
"the obscure we see eventually, the completely apparent takes longer."" 
Peter D. Mitchell, Nobel Lecture 1978 


Mitchell got the Nobel Prize for elucidating the details of one of the biggest 
mysteries of life — How does the energy in NADH and FADH) get 
converted to ATP. His explanation, now known as the chemiosmotic 
hypothesis is quite simple in concept, and involves things you already 
understand, like solute gradients across membranes and redox reactions. 
You have just read about two pathways in glucose catabolism—glycolysis 
and the Kreb's cycle cycle—that generate ATP. Most of the ATP generated 
during the aerobic catabolism of glucose, however, is not generated directly 
from these pathways. Rather, it is derived from a process that begins with 
moving electrons through a series of electron transporters that undergo 
redox reactions. This causes hydrogen ions to accumulate within the 
intermembrane space. Therefore, a concentration gradient forms; this 
concentration gradient represents potential energy. That energy is dissipated 
when hydrogen ions diffuse back into the mitochondrial matrix, passing 
through a channel formed by the ATP synthase embedded in the 
membrane. As they flow through, the ATP synthase uses that energy to 
make ATP, just like a water-powered generator uses water flow to generate 
electricity. The current of hydrogen ions powers the catalytic action of ATP 
synthase, which phosphorylates ADP, producing ATP. 


Electron Transport Chain 


The electron transport chain ((link]) is the last component of aerobic 
cellular respiration and is the only part of glucose metabolism that uses 
atmospheric oxygen. Oxygen continuously diffuses into plants and single- 
celled organisms; in animals, it enters the body through the respiratory 


system. Electron transport is a series of redox reactions that resemble a 
relay race or bucket brigade; electrons are passed rapidly from one 
component to the next, eventually arriving at the endpoint of the chain 
where the electrons are used to reduce molecular oxygen, producing water. 
There are four complexes composed of proteins, labeled I through IV in 
[link], and the aggregation of these four complexes, together with 
associated mobile, accessory electron carriers, is called the electron 
transport chain. The electron transport chain is present in multiple copies in 
the inner mitochondrial membrane of eukaryotes and the plasma membrane 
of prokaryotes. 


Electron Transport Chain 


Intermembrane space 


ae )/ 
i 


Mir eer 
Wi WV ECU EY 


Mitochondrial matrix Inner mitochondrial membrane 


The electron transport chain is a 
series of electron transporters 
embedded in the inner 
mitochondrial membrane that 
shuttles electrons from NADH and 
FADH)> to molecular oxygen. In 
the process, protons are pumped 
from the mitochondrial matrix to 
the intermembrane space, and 
oxygen is reduced to form water. 


Complex I 


To start, two electrons are carried to the first complex aboard NADH. This 
complex, labeled I, is composed of flavin mononucleotide (FMN) and an 
iron-sulfur (Fe-S)-containing protein. FMN, which is derived from vitamin 
Bo also called riboflavin, is one of several prosthetic groups or co-factors in 
the electron transport chain. A prosthetic group is a non-protein molecule 
required for the activity of a protein. Prosthetic groups are organic or 
inorganic, non-peptide molecules bound to a protein that facilitate its 
function; prosthetic groups include co-enzymes, which are the prosthetic 
groups of enzymes. The enzyme in complex I is NADH dehydrogenase and 
is a very large protein, containing 45 amino acid chains. Complex I can 
pump four hydrogen ions across the membrane from the matrix into the 
intermembrane space, and it is in this way that the hydrogen ion gradient is 
established and maintained between the two compartments separated by the 
inner mitochondrial membrane. 


Q and Complex II 


Complex II directly receives FADH), which does not pass through complex 
I. The compound connecting the first and second complexes to the third is 
ubiquinone (Q). The Q molecule is lipid soluble and freely moves through 
the hydrophobic core of the membrane. Once it is reduced, (QH)), 
ubiquinone delivers its electrons to the next complex in the electron 
transport chain. Q receives the electrons derived from NADH from complex 
I and the electrons derived from FADH) from complex II, including 
succinate dehydrogenase. This enzyme and FADH> form a small complex 
that delivers electrons directly to the electron transport chain, bypassing the 
first complex. Since these electrons bypass and thus do not energize the 
proton pump in the first complex, fewer ATP molecules are made from the 
FADH) electrons. The number of ATP molecules ultimately obtained is 
directly proportional to the number of protons pumped across the inner 
mitochondrial membrane. 


Complex III 


The third complex is composed of cytochrome b, another Fe-S protein, 
Rieske center (2Fe-2S center), and cytochrome c proteins; this complex is 
also called cytochrome oxidoreductase. Cytochrome proteins have a 
prosthetic group of heme. The heme molecule is similar to the heme in 
hemoglobin, but it carries electrons, not oxygen. As a result, the iron ion at 
its core is reduced and oxidized as it passes the electrons, fluctuating 
between different oxidation states: Fe’* (reduced) and Fe*** (oxidized). 
The heme molecules in the cytochromes have slightly different 
characteristics due to the effects of the different proteins binding them, 
giving slightly different characteristics to each complex. Complex III 
pumps protons through the membrane and passes its electrons to 
cytochrome c for transport to the fourth complex of proteins and enzymes 
(cytochrome c is the acceptor of electrons from Q; however, whereas Q 
carries pairs of electrons, cytochrome c can accept only one at a time). 


Complex IV 


The fourth complex is composed of cytochrome proteins c, a, and a3. This 
complex contains two heme groups (one in each of the two cytochromes, a, 
and a3) and three copper ions (a pair of Cu, and one Cup in cytochrome a3). 
The cytochromes hold an oxygen molecule very tightly between the iron 
and copper ions until the oxygen is completely reduced. The reduced 
oxygen then picks up two hydrogen ions from the surrounding medium to 
make water (H2O). The removal of the hydrogen ions from the system 
contributes to the ion gradient used in the process of chemiosmosis. 


Chemiosmosis 


In chemiosmosis, the free energy from the series of redox reactions just 
described is used to pump hydrogen ions (protons) across the membrane 
(from inside the matrix into the intermembrane space). The uneven 
distribution of H* ions across the membrane establishes both concentration 
and electrical gradients (thus, an electrochemical gradient), sue to the 


hydrogen ions’ positive charge and their aggregation on one side of the 
membrane. This electrochemical gradient is a form of potential energy, and 
its discovery was a key step in Mitchell's elucidation of the details of 
oxidative phosphorylation. 


If the membrane was not a barrier to the movement of the hydrogen ions, 
the ions would diffuse back across into the matrix, driven by their 
electrochemical gradient. But recall that many ions cannot diffuse through 
the nonpolar regions of phospholipid membranes without the aid of ion 
channels. Similarly, hydrogen ions in the intermembrane space can only 
pass through the inner mitochondrial membrane through an integral 
membrane protein called ATP synthase ([link]). This complex protein acts 
as a tiny generator, turned by the force of the hydrogen ions diffusing down 
their electrochemical gradient via a channel in the protein. This powers an 
actual rotation of parts of the enzyme; the rotation of parts of this molecular 
machine facilitates the addition of a phosphate to ADP, forming ATP. In the 
absence of a hydrogen ion gradient, the rotation stops and no ATP is made. 


ATP Synthase 


Intermembrane Inner mitochondrial 
space membrane 


Vatarpvarprarecarppipay: Wp p'p'p'P aah ata hatang? 


UAL eR 


Mitochondrial 
matrix 


ATP synthase is a complex, 
molecular machine that uses a 
proton (H*) gradient to form ATP 
from ADP and inorganic 
phosphate (Pi). (Credit: 
modification of work by Klaus 
Hoffmeier) 


Chemiosmosis ([link]) is used to generate 90 percent of the ATP made 
during aerobic cellular respiration; it is also the method used in the light 
reactions of photosynthesis to harness the energy of sunlight in the process 
of photophosphorylation. Recall that the production of ATP using the 
process of chemiosmosis in mitochondria is called oxidative 
phosphorylation. The overall result of these reactions is the production of 
about 32 ATP from the energy of the electrons removed from hydrogen 
atoms ([link]). These electrons were originally part of a glucose molecule. 
At the end of the pathway, the electrons are used to reduce an oxygen 
molecule to oxygen ions. The extra electrons on the oxygen attract 
hydrogen ions (protons) from the surrounding medium, and water is 
formed. 


Intermembrane space 


+ + + 
H one 


He Hh rea na es ahah y WV WWW eit igs. 
WU i 1) im Deion 
ATP FADH2 


synthase Gene FAD 0; HO 
NAD* + H* 
Kreb's 


Matrix ae, 


ULL 


=f 
= 


Wu uu) 
veil 


In oxidative phosphorylation, the hydrogen 

ion electrochemical gradient, generated by 

the electron transport chain, is used by ATP 
synthase to form ATP. 


Glucose 


rit i a ne 
: : || \Acetyl-GoA! | 
Oxidative pee enemy 


| . are | \\ " 
\“\s : ‘ | tii 
m Phosphory- Ba ay | CO 


———— 


Oxidative Phosphorylation 


This image is an overview of oxidative phosphorylation. During this 
stage, the electrons from NADH and FADH? are used to produce a 
large amount of ATP (~32). (Image by Eva Horne and Robert Bear) 


ATP Yield 


The number of ATP molecules generated from the catabolism of glucose 
can be variable. For example, the number of hydrogen ions that the electron 
transport chain complexes can pump through the membrane varies between 
species. Another source of variance stems from the shuttle of electrons 
across the membranes of the mitochondria. (The NADH generated from 
glycolysis cannot easily enter mitochondria.) Thus, electrons are picked up 
on the inside of mitochondria by either NAD* or FAD*. As you have 
learned earlier, these FAD* molecules carry electrons that are lower in 
energy than those on NADH; consequently, fewer ATP molecules are 
generated when FAD” acts as a carrier. NAD* is used as the electron 
transporter in the liver and FAD” acts in the brain. Assuming optimal ATP 
production, a net of 2 are formed in glycolysis, 2 are formed in the Kreb's 
cycle, and 32 produced during oxidative phophorylation ({link]). The total 
amount of ATP formed form 1 molecule of glucose is generally around 36 
under optimal conditions. 


Cytoplasm 
H,O O, 


Y 


Oxidative 


Phosphory- 
lation 


Aerobic Cellular Respiration 


This image is an overview of aerobic cellular respiration showing the 
number of ATP produced by the various steps of the process. 
Assuming optimal conditions, there are 36 ATP molecules produced 
for each molecule of glucose entering aerobic cellular respiration. 
(Image by Eva Horne and Robert Bear) 


Another factor that affects the yield of ATP molecules generated from 
glucose is the fact that intermediate compounds and electron carriers in 
these pathways are used for other purposes. Glucose catabolism connects 
with the pathways that build or break down all other biochemical 
compounds in cells, and the result is that some metabolites (e.g. pyruvate) 
are shuttled off for other purposes. Additionally, sugars other than glucose 
are fed into various steps in the glycolytic pathway for energy extraction. 
The five-carbon sugars that form nucleic acids are made from intermediates 


in glycolysis. Certain nonessential amino acids can be made from 
intermediates of both glycolysis and the Krebs cycle. Lipids, such as 
cholesterol and triglycerides, are also made from acetyl-CoA, and both 
amino acids and triglycerides are broken down for energy, feeding into 
these pathways at various places. NADH is used by other redox reactions in 
cells, which means that not all of the high energy electrons liberated from 
glucose are used in oxidative phosphorylation. So the tidy pictures above 
don't really reflect the complexity of metabolism in a living cell. So the 
relationship between glucose breakdown and ATP production is like all 
relationships: "It's complicated." 


Codependency of Photosynthesis and Aerobic Cellular 
Respiration 


As you may have noticed, the substrates of aerobic cellular respiration are 
the products of photosynthesis, and the substrates of photosynthesis are the 
products of aerobic cellular respiration ([link]). These two processes are 
interdependent; they have been evolving with one another for a very long 
time and are important components of the carbon cycle and obviously the 
flow of energy. In this section, we will take a closer look at the 
codependency of photosynthesis and cellular respiration. 


H,O O, Cytoplasm 


Oxidative 
Phosphory- 


Aerobic Cellular Respiration 


This image shows the interrelatedness of photosynthesis and aerobic 


cellular respiration Note how the the two processes are almost mirror 
images of each other. (Image by Eva Horne and Robert Bear) 


The first point of interaction is the cycling of water and oxygen. During 
photosynthesis, oxygen gas is produced and the source of the oxygen atoms 
is the reactant water. The oxygen is formed in the initial step of 
photosynthesis, when photosystem II splits a water molecule into oxygen 
gas, hydrogen ions and electrons. In the light dependent reactions on the 
thylakoid membrane, light energy is absorbed and transferred to ATP and 
NADP. The light energy is transferred to chemical energy during this 
process. In aerobic cellular respiration, the roles are reversed: oxygen is the 
reactant, and water is the product. The aerobic cellular respiration process 
uses oxygen in the final (not initial) step, when it merges (rather than 
splitting) with the electrons and hydrogen ions during oxidative 
phosphorylation. The cycling of water and oxygen between photosynthesis 
and aerobic cellular respiration is the source of electrons that harvest, store 
and transfer energy. 


Another product of photosynthesis is Glucose (carbohydrate). In the Calvin 
cycle, carbohydrates are produced by fixing carbon dioxide (reactant) and 
by adding energy from ATP and NADPH. During aerobic cellular 
respiration, NADH and FADH) capture the energy stored in glucose 
(reactant). The captured energy in NADH and FADH)j is then used during 
oxidative phospholrylation to produce ATP. This process of energy capture 
also releases a waste product - carbon dioxide. So energy from the sun is 
used to make glucose from COs, which is a nutrient for the plant. The 
product of photosynthesis (glucose) contains that nutrient AND the energy 
derived from sunlight; glcuose is thus a high energy nutrient for 
heterotrophic organisms. These organisms release the nutrient as CO» and 
use some of the energy to do cellular work. Other energy is lost as heat. It 
should be obvious that nutrients cycle between autotrophs and heterotrophs, 
while energy moves in a one-way direction from autotrophs to heterotrophs. 


Photosynthesis and aerobic cellular respiration are codependent; they rely 
upon use each other’s products and byproducts and are essentially the 


opposites of each other. Neither process can happen without the other 
because if there is no carbon dioxide, photosynthesis cannot proceed; and if 
there is no oxygen, aerobic cellular respiration cannot proceed. The 
exergonic reactions of cellular respiration (glycolysis, Kreb’s cycle and 
oxidative phosphorylation) mirror the energonic reactions of photosynthesis 
(Light Dependent Reactions and Calvin cycle). As we learned on the 
ecosystem level, nutrients cycle and energy flows. The same is true on the 
cellular level: nutrients cycle and energy flows. 


Metabolism Without Oxygen 


"Not all chemicals are bad. Without chemicals such as hydrogen and 
oxygen, for example, there would be no way to make water, a vital 
ingredient in beer." - Dave Barry 


The other vital ingredient in beer, of course, is ethanol. And ethanol is one 
of the more important products of anaerobic respiration. Other compounds, 
such as lactic acid, are also metabolic by-products of respiration in the 
absence of oxygen. The key purpose of all of these metabolic pathways is 
the need to regenerate NAD from the NADH produced during glycolysis. In 
aerobic respiration, NADH donates those electrons to the electron transfer 
chain. Recall that the final electron acceptor in that pathway is an oxygen 
molecule, O>. If oxygen is present, then ATP will be produced using the 
energy of high-energy electrons carried by NADH or FADH> to the electron 
transport chain. If oxygen is not present, NADH must be reoxidized to 
NAD‘ for reuse as an electron carrier for the glycolytic pathway to 
continue. How is this done? Some living systems use an organic molecule 
as the final electron acceptor. Processes that use an organic molecule to 
regenerate NAD* from NADH are collectively referred to as fermentation 
(anaerobic metabolism). In contrast, some living systems use an inorganic 
molecule as a final electron acceptor of the electron transport chain, and this 
process is called anaerobic cellular respiration in which organisms 
convert energy for their use in the absence of oxygen. 


Anaerobic Metabolism 


Certain prokaryotes, including some species of bacteria and Archaea, use 
anaerobic respiration. For example, the group of Archaea called 
methanogens reduces carbon dioxide to methane to oxidize NADH. These 
microorganisms are found in soil and in the digestive tracts of ruminants, 
such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea, 
most of which are anaerobic ( [link]), reduce sulfate to hydrogen sulfide to 
regenerate NAD* from NADH. 


The green color seen in these coastal waters 
is from an eruption of hydrogen sulfide- 
producing bacteria. These anaerobic, sulfate- 
reducing bacteria release hydrogen sulfide 
gas as they decompose algae in the water. 
(credit: modification of work by NASA/Jeff 
Schmaltz, MODIS Land Rapid Response 
Team at NASA GSFC, Visible Earth 
Catalog of NASA images) 


Lactic Acid Fermentation 


The fermentation method used by animals and certain bacteria, like those in 
yogurt, is lactic acid fermentation ( [link]). This type of fermentation is 
used routinely in mammalian red blood cells and in skeletal muscle that has 
an insufficient oxygen supply to allow aerobic respiration to continue (that 
is, in muscles used to the point of fatigue). In muscles, lactic acid 
accumulation must be removed by the blood circulation and the lactate 
brought to the liver for further metabolism. 


Cytoplasm 


Lactic acid fermentation is common in muscle cells that 
have run out of oxygen. (Image by Robert Bear) 


Alcohol Fermentation 


Another familiar fermentation process is alcohol fermentation ( [link]) that 
produces ethanol, an alcohol. The first chemical reaction of alcohol 
fermentation is the following (CO> does not participate in the second 
reaction): 


The first reaction is catalyzed by pyruvate decarboxylase, a cytoplasmic 
enzyme, with a coenzyme of thiamine pyrophosphate (TPP, derived from 
vitamin B, and also called thiamine). A carboxyl group is removed from 
pyruvate, releasing carbon dioxide as a gas. The loss of carbon dioxide 
reduces the size of the molecule by one carbon, making acetaldehyde. The 
second reaction is catalyzed by alcohol dehydrogenase to oxidize NADH to 
NAD* and reduce acetaldehyde to ethanol. The fermentation of pyruvate by 
yeast produces the ethanol found in alcoholic beverages. Ethanol tolerance 
of yeast is variable, ranging from about 5 percent to 21 percent, depending 
on the yeast strain and environmental conditions. 


YAP 


Alcohol fermentation is occurs in fungi and plants with 
carbon dioxide and alcohol as the byproducts. (Image by 
Robert Bear) 


= Cytoplasm a - 


Other Types of Fermentation 


Other fermentation methods occur in bacteria. Many prokaryotes are 
facultatively anaerobic. This means that they can switch between aerobic 
respiration and fermentation, depending on the availability of oxygen. 
Certain prokaryotes, like Clostridia, are obligate anaerobes. Obligate 
anaerobes live and grow in the absence of molecular oxygen. Oxygen is a 
poison to these microorganisms and kills them on exposure. It should be 
noted that all forms of fermentation, except lactic acid fermentation, 
produce gas. The production of particular types of gas is used as an 
indicator of the fermentation of specific carbohydrates, which plays a role 
in the laboratory identification of the bacteria. Various methods of 
fermentation are used by assorted organisms to ensure an adequate supply 
of NAD* for the sixth step in glycolysis. Without these pathways, that step 
would not occur and no ATP would be harvested from the breakdown of 
glucose. 


Connections of Carbohydrate, Protein, and Lipid Metabolic Pathways 


Introduction 

" SIR TOBY: Does not our lives consist of the four elements? / SIR 
ANDREW: Faith, so they say; but I think it rather consists of eating and 
drinking. / SIR TOBY: Thou'rt a scholar; let us therefore eat and drink. " 
William Shakespeare, Twelfth Night 


You have learned about the catabolism of glucose, which provides energy to 
living cells. But when you eat and drink, as advised by Sir Toby, you 
consume more than glucose for food. How does a turkey/avocado sandwich 
end up as ATP in your cells? This happens because all of the catabolic 
pathways for carbohydrates, proteins, and lipids eventually connect into 
glycolysis and the Krebs cycle pathways (see [link]). Metabolic pathways 
should be thought of as porous—that is, substances enter from other 
pathways, and intermediates leave for other pathways. These pathways are 
not closed systems. Many of the substrates, intermediates, and products in a 
particular pathway are reactants in other pathways. 


Connections of Other Sugars to Glucose Metabolism 


Glycogen, a polymer of glucose, is an energy storage molecule in animals. 
When there is adequate ATP present, excess glucose is shunted into 
glycogen for storage. Glycogen is made and stored in both liver and muscle. 
The glycogen will be hydrolyzed into glucose monomers (G-1-P) if blood 
sugar levels drop. The presence of glycogen as a source of glucose allows 
ATP to be produced for a longer period of time during exercise. Glycogen is 
broken down into G-1-P and converted into G-6-P in both muscle and liver 
cells, and this product enters the glycolytic pathway. 


Sucrose is a disaccharide with a molecule of glucose and a molecule of 
fructose bonded together with a glycosidic linkage. Fructose is one of the 
three dietary monosaccharides, along with glucose and galactose (which is 
part of the milk sugar, the disaccharide lactose), which are absorbed directly 
into the bloodstream during digestion. The catabolism of both fructose and 
galactose produces the same number of ATP molecules as glucose. 


Connections of Proteins to Glucose Metabolism 


Proteins are hydrolyzed by a variety of enzymes in cells. Most of the time, 
the amino acids are recycled into the synthesis of new proteins. If there are 
excess amino acids, however, or if the body is in a state of starvation, some 
amino acids will be shunted into the pathways of glucose catabolism 
({link]). Each amino acid must have its amino group removed prior to entry 
into these pathways. The amino group is converted into ammonia. In 
mammals, the liver synthesizes urea from two ammonia molecules and a 
carbon dioxide molecule. Thus, urea is the principal waste product in 
mammals produced from the nitrogen originating in amino acids, and it 
leaves the body in urine. 


Phosphoenolpyruvate Alanine Glycine Threonine 
Cysteine Serine Tryptophan 


fl ovate 
ine 


Glucose Acetyl CoA [> = Acetoacetate 
Leucine 
Lysine 
Phenylalanine 
Oxaloacetate Citrate Tyrosine 
Tryptophan 
Asparagine / \ 
Aspartate Anis Peal 
: rginine Proline 
Malate onal Histidine Glutamine 


Fumarate a-Ketoglutarate Glutamate 
Tyrosine \ F F / Isoleucine Valine 
Phenylalanine a ee a CoA Methionine Threonine 


The carbon skeletons of certain amino acids (indicated in 
boxes) derived from proteins can feed into the Krebs 
cycle. (credit: modification of work by Mikael 
Haggstrém) 


Connections of Lipid and Glucose Metabolisms 


The lipids that are connected to the glucose pathways are cholesterol and 
triglycerides. Cholesterol is a lipid that contributes to plasma membrane 
flexibility and is a precursor of steroid hormones. The synthesis of 
cholesterol starts with acetyl groups and proceeds in only one direction. The 
process cannot be reversed. 


Triglycerides are a form of long-term energy storage in animals. 
Triglycerides are made of glycerol and three fatty acids. Animals can make 
most of the fatty acids they need. Triglycerides can be both made and 
broken down through parts of the glucose catabolism pathways. Glycerol 
can be phosphorylated to glycerol-3-phosphate, which continues through 
glycolysis. Fatty acids are catabolized in a process called beta-oxidation 
that takes place in the matrix of the mitochondria and converts their fatty 
acid chains into two carbon units of acetyl groups. The acetyl groups are 
picked up by CoA to form acetyl-CoA that proceeds into the Krebs cycle. 


<€ ——— 
Acetyl-CoA 


~ 
BET Amino Acids 


Glycogen from the liver and muscles, hydrolyzed 
into glucose-1-phosphate, together with fats and 
proteins, can feed into the catabolic pathways for 


carbohydrates. Work by Eva Horne and Robert A. 
Bear. 


Note: 

Evolution Connection 

Pathways of Photosynthesis and Cellular Metabolism 

The processes of photosynthesis and cellular metabolism consist of several 
very complex pathways. It is generally thought that the first cells arose in 
an aqueous environment—a “soup” of nutrients—probably on the surface 
of some porous clays. If these cells reproduced successfully and their 
numbers climbed steadily, it follows that the cells would begin to deplete 
the nutrients from the medium in which they lived as they shifted the 
nutrients into the components of their own bodies. This hypothetical 
situation would have resulted in natural selection favoring those organisms 
that could exist by using the nutrients that remained in their environment 
and by manipulating these nutrients into materials upon which they could 
survive. Selection would favor those organisms that could extract maximal 
value from the nutrients to which they had access. 

An early form of photosynthesis developed that harnessed the sun’s energy 
did not use water as a source of hydrogen atoms, and did not produce free 
oxygen (anoxygenic photosynthesis). Early photosynthesis did not produce 
free oxygen because it did not use water as the source of hydrogen ions; 
instead, it used materials like hydrogen sulfide and consequently produced 
sulfur. It is thought that glycolysis developed at this time and could take 
advantage of the simple sugars being produced, but these reactions were 
unable to fully extract the energy stored in the carbohydrates. The 
development of glycolysis probably predated the evolution of 
photosynthesis, as it was well suited to extract energy from materials 
spontaneously accumulating in the “primeval soup.” A later form of 
photosynthesis used water as a source of electrons and hydrogen, and 
generated free oxygen. Over time, the atmosphere became oxygenated, but 
not before the oxygen released oxidized metals in the ocean and created a 
“rust” layer in the sediment, permitting the dating of the rise of the first 


oxygenic photosynthesizers. Living things adapted to exploit this new 
atmosphere that allowed aerobic respiration as we know it to evolve. When 
the full process of oxygenic photosynthesis developed and the atmosphere 
became oxygenated, cells were finally able to use the oxygen expelled by 
photosynthesis to extract considerably more energy from the sugar 
molecules using the Krebs cycle and oxidative phosphorylation. 


Prokaryote Structure 
By the end of this section, you will be able to do the following: 


e Describe the basic structure of a typical prokaryote 
e Describe important differences in structure between Archaea and 
Bacteria 


"For the first half of geological time our ancestors were bacteria. Most 
creatures still are bacteria, and each one of our trillions of cells is a colony 
of bacteria." Richard Dawkins 


There are many differences between prokaryotic and eukaryotic cells. The 
name "prokaryote" suggests that prokaryotes are defined by exclusion— 
they are not eukaryotes, or organisms whose cells contain a nucleus and 
other internal membrane-bound organelles. However, all cells have four 
common structures: the plasma membrane, which functions as a barrier for 
the cell and separates the cell from its environment; the cytoplasm, a 
complex solution of organic molecules and salts inside the cell; a double- 
stranded DNA genome, the informational archive of the cell; and 
ribosomes, where protein synthesis takes place. Prokaryotes come in 
various shapes, but many fall into three categories: cocci (spherical), bacilli 
(rod-shaped), and spirilli (spiral-shaped) ({link]). 


(a) (b) (c) 


Common prokaryotic cell types. Prokaryotes fall into three 
basic categories based on their shape, visualized here using 
scanning electron microscopy: (a) cocci, or spherical (a pair is 
shown); (b) bacilli, or rod-shaped; and (c) spirilli, or spiral- 
shaped. (credit a: modification of work by Janice Haney Carr, 


Dr. Richard Facklam, CDC; credit c: modification of work by 
Dr. David Cox; scale-bar data from Matt Russell) 


The Prokaryotic Cell 


Recall that prokaryotes are unicellular organisms that lack membrane- 
bound organelles or other internal membrane-bound structures ({link]). 
Their chromosome—usually single—consists of a piece of circular, double- 
stranded DNA located in an area of the cell called the nucleoid. Most 
prokaryotes have a cell wall outside the plasma membrane. The cell wall 
functions as a protective layer, and it is responsible for the organism’s 
shape. Some bacterial species have a capsule outside the cell wall. The 
capsule enables the organism to attach to surfaces, protects it from 
dehydration and attack by phagocytic cells, and makes pathogens more 
resistant to our immune responses. Some species also have flagella 
(singular, flagellum) used for locomotion, and pili (singular, pilus) used for 
attachment to surfaces including the surfaces of other cells. Plasmids, which 
consist of extra-chromosomal DNA, are also present in many species of 
bacteria and archaea. 


Cell 
membrane 


Ribosome 


Chromosome Nucleoid region 
(DNA) 


The features of a typical 
prokaryotic cell. Flagella, 


capsules, and pili are not found in 
all prokaryotes. 


Recall that prokaryotes are divided into two different domains, Bacteria and 
Archaea, which together with Eukarya, comprise the three domains of life 


(Link]). 


Euryarchaeotes 
Crenachaeotes 
Nanoarchaeotes 
Korarchaeotes 


Proteobacteria 
Chlamydias 
Spirochetes 
Cyanobacteria 
Gram-Positive bacteria 


The three domains of living organisms. Bacteria 
and Archaea are both prokaryotes but differ 
enough to be placed in separate domains. An 
ancestor of modern Archaea is believed to have 
given rise to Eukarya, the third domain of life. 
Major groups of Archaea and Bacteria are 
shown. 


Characteristics of bacterial phyla are described in [link] and [link]. Major 
bacterial phyla include the Proteobacteria, the Chlamydias, the 
Spirochaetes, the photosynthetic Cyanobacteria, and the Gram-positive 
bacteria. The Proteobacteria are in turn subdivided into several classes, 
from the Alpha- to the Epsilon proteobacteria. Eukaryotic mitochondria are 
thought to be the descendants of alphaproteobacteria, while eukaryotic 
chloroplasts are derived from cyanobacteria. Archaeal phyla are described 
in [Link]. 


Bacteria of Phylum Proteobacteria 


Alpha Proteobacteria Rhizobium 

Some species are photoautotrophic Nitrogen-fixing endosymbiont 

but some are symbionts of plants associated with the roots of legumes 

and animals and others are 

pathogens. Eukaryotic mitochondria Rickettsia 

are thought be derived from bacteria Obligate intracellular parasite that 

in this group. causes typhus and Rocky Mountain 
Spotted Fever (but not rickets, 
which is caused by Vitamin C Rickettsia rickettsia, stained red, grow 
deficiency) inside a host cell. 


Beta Proteobacteria Nitrosomas 
This group of bacteria is diverse. Species from this group oxidize 
Some species play an important ammonia into nitrite. 
role in the nitrogen cycle. 
Spirillum minus 
Causes rat-bite fever 


Gamma Proteobacteria Escherichia coli 
Many are beneficial symbionts that Normally beneficial microbe of 
populate the human gut, but others the human gut, but some strains 
are familiar human pathogens. cause disease 
Some species from this subgroup 
oxidize sulfur compounds. Salmonella 
Certain strains cause food 
poisoning or typhoid fever 
Vibrio cholera 
Yersinia pestis 
Causative agent of Bubonic plague 


Psuedomonas aeruginosa 
Causes lung infections 


Vibrio cholera 
Causative agent of cholera 


Chromatium 
Sulfur-producing bacteria that 
oxidize sulfur, producing H»S 


Delta Proteobacteria Myxobacteria 
Some species generate a Generate spore-forming fruiting 
spore-forming fruiting body in bodies in adverse conditions 
adverse conditions. Others 
reduce sulfate and sulfur. Desulfovibrio vulgaris 
Aneorobic, sulfate-reducing L* Le 
| — 
bacterium > ~ 500 nm" 


Desulfovibrio vulgaris 


Epsilon Proteobacteria Campylobacter 

Many species inhabit the digestive Causes blood poisoning and 

tract of animals as symbionts or intestinal inflammation 

pathogens. Bacteria from this group f - 

have been found in deep-sea Heliobacter pylori 

hydrothermal vents and cold seep Causes stomach ulcers 

habitats. 9 e 500 hm 


Campylobacter 


The Proteobacteria. Phylum Proteobacteria is one of up to 52 
bacteria phyla. Proteobacteria is further subdivided into five 
classes, Alpha through Epsilon. (credit “Rickettsia rickettsia”: 
modification of work by CDC; credit “Spirillum minus”: 
modification of work by Wolframm Adlassnig; credit “Vibrio 
cholera”: modification of work by Janice Haney Carr, CDC; 


credit “Desulfovibrio vulgaris”: modification of work by 
Graham Bradley; credit “Campylobacter”: modification of 
work by De Wood, Pooley, USDA, ARS, EMU; scale-bar data 


from Matt Russell) 


Bacteria: Chlamydia, Spirochaetae, Cyanobacteria, and Gram-positive 


Chlamydias 

All members of this group are 

obligate intracellular parasites of animal 
cells. Cells walls lack peptidoglycan. 


Spirochetes 

Most members of this species, 

which has spiral-shaped cells, are 
free-living aneaerobes, but some are 
pathogenic. Flagella run lengthwise in the 
periplasmic space between the inner and 
outer membrane. 


Cyanobacteria 

Also known as blue-green algae, 

these bacteria obtain their energy through 
photosynthesis. They are ubiquitous, 
found in terrestrial, marine, and freshwater 
environments. Eukaryotic chloroplasts are 
thought be derived from bacteria in this 
group. 


Gram-positive Bacteria 

Soil-dwelling members of this subgroup 
decompose organic matter. Some species 
cause disease. They have a thick cell wall 
and lack an outer membrane. 


Chlamydia trachomatis 
Common sexually transmitted 
disease that can lead to blindness 


Treponema pallidum 
Causative agent of syphilis 


Borrelia burgdorferi 
Causative agent of Lyme disease 


Prochlorococcus 

Believed to be the most abundant 
photosynthetic organism on earth; 
responsible for generating half 
the world’s oxygen 


Bacillus anthracis 
Causes anthrax 


Clostridium botulinum 
Causes Botulism 


Clostridium difficile 
Causes diarrhea during antibiotic 
therapy 


Streptomyces 

Many antibiotics, including 
streptomyocin, are derived from 
these bacteria. 


Mycoplasmas 

These tiny bacteria, the smallest 
known, lack a cell wall. 

Some are free-living, and some 
are pathogenic. 


—<s 


b — \ 
CZ #10 yum 


In this pap smear, Chlamydia trachomatis 
appear as pink inclusions inside cells. 


Treponema pallidum 


2 Om 
Phormidium 


A. 


, “© °70 pn 
Clostridium difficile 


Other bacterial phyla. Chlamydia, Spirochetes, Cyanobacteria, 
and Gram-positive bacteria are described in this table. Note 


that bacterial shape is not phylum-dependent; bacteria within a 
phylum may be cocci, rod-shaped, or spiral. (credit 
“Chlamydia trachomatis”: modification of work by Dr. Lance 
Liotta Laboratory, NCI; credit “Treponema pallidum”: 
modification of work by Dr. David Cox, CDC; credit 
“Phormidium”: modification of work by USGS; credit 
“Clostridium difficile”: modification of work by Lois S. 
Wiggs, CDC; scale-bar data from Matt Russell) 


Euryarchaeota 

This phylum includes 
methanogens, which produce 
methane as a metabolic waste 
product, and halobacteria, 
which live in an extreme saline 
environment. 


Crenarchaeota 

Members of the ubiquitous 
phylum play an important role 

in the fixation of carbon. Many 
members of this group are 
sulfur-dependent extremophiles. 
Some are thermophilic or 
hyperthermophilic. 


Nanoarchaeota 

This group currently contains 
only one species, 
Nanoarchaeum equitans. 


Korarchaeota 

Members of this phylum, 
considered to be one of the 
most primitive forms of life, 
have only been found in the 
Obsidian Pool, a hot spring at 
Yellowstone National Park. 


Methanogens 

Methane production causes 
flatulence in humans and other 
animals. 


Halobacteria 

Large blooms of this salt-loving 
archaea appear reddish due to 
the presence of bacterirhodopsin 
in the membrane. 
Bacteriorhodopsin is related to 
the retinal pigment rhodopsin. 


Sulfolobus 

Members of this genus grow 

in volcanic springs at 
temperatures between 75° and 
80°C and at a pH between 

2 and 3. 


ium 
Sulfolobus being infected by bacteriophage 


Nanoarchaeum equitans 

This species was isolated from 
the bottom of the Atlantic Ocean 
and from a hydrothermal vent 
at Yellowstone National Park. 

It is an obligate symbiont with 
Ignicoccus, another species of 
archaea. 


Nanoarchaeum equitans (small dark spheres) are 
in contact with their larger host, /gnicoccus. 


No members of this species 
have been cultivated. 


y 
wv a . 
This image shows a variety of korarchaeota species 
from the Obsidian Pool at Yellowstone National Park. 


Archaeal phyla. Archaea are separated into four phyla: the 
Korarchaeota, Euryarchaeota, Crenarchaeota, and 
Nanoarchaeota. (credit “Halobacterium”: modification of 
work by NASA; credit “Nanoarchaeotum equitans”: 
modification of work by Karl O. Stetter; credit “Korarchaeota” 
modification of work by Office of Science of the U.S. Dept. of 
Energy; scale-bar data from Matt Russell) 


The Plasma Membrane of Prokaryotes 


The prokaryotic plasma membrane is a thin lipid bilayer (6 to 8 
nanometers) that completely surrounds the cell and separates the inside 
from the outside. Its selectively permeable nature keeps ions, proteins, and 
other molecules within the cell and prevents them from diffusing into the 
extracellular environment, while other molecules may move through the 
membrane. Recall that the general structure of a cell membrane is a 
phospholipid bilayer composed of two layers of lipid molecules. In archaeal 
cell membranes, isoprene (phytanyl) chains linked to glycerol replace the 
fatty acids linked to glycerol in bacterial membranes. Some archaeal 
membranes are lipid monolayers instead of bilayers ({link]). 


Phospholipid from ® Phytanyl 


Archaea 7 sidechain 


@® Ether linkage 


Phospholipid from Bacteria Ester linkage 


and Eukarya 


Glycerol 
Phosphate group 


OS SE OO 
OES SED Oa 
OS SD ORE 


Phospholipid bilayer from Phospholipid bilayer from 
Bacteria and Eukarya Archaea 


Bacterial and archaeal 
phospholipids. Archaeal 


phospholipids differ from those 
found in Bacteria and Eukarya in 
two ways. First, they have 
branched phytanyl sidechains 
instead of linear ones. Second, an 
ether bond instead of an ester bond 
connects the lipid to the glycerol. 


The Cell Wall of Prokaryotes 


The cytoplasm of prokaryotic cells has a high concentration of dissolved 
solutes. Therefore, the osmotic pressure within the cell is relatively high. 
The cell wall is a protective layer that surrounds some cells and gives them 
shape and rigidity. It is located outside the cell membrane and prevents 
osmotic lysis (bursting due to increasing volume). The chemical 
composition of the cell wall varies between Archaea and Bacteria, and also 
varies between bacterial species. 


Bacterial cell walls contain peptidoglycan, composed of polysaccharide 
chains that are cross-linked by unusual peptides containing both L- and D- 
amino acids including D-glutamic acid and D-alanine. (Proteins normally 
have only L-amino acids; as a consequence, many of our antibiotics work 
by mimicking D-amino acids and therefore have specific effects on 
bacterial cell-wall development.) There are more than 100 different forms 
of peptidoglycan. S-layer (surface layer) proteins are also present on the 
outside of cell walls of both Archaea and Bacteria. 


Bacteria are divided into two major groups: Gram positive and Gram 
negative, based on their reaction to Gram staining. Note that all Gram- 
positive bacteria belong to one phylum; bacteria in the other phyla 
(Proteobacteria, Chlamydias, Spirochetes, Cyanobacteria, and others) are 
Gram-negative. The Gram staining method is named after its inventor, 
Danish scientist Hans Christian Gram (1853-1938). The different bacterial 
responses to the staining procedure are ultimately due to cell wall structure. 


Gram-positive organisms typically lack the outer membrane found in 
Gram-negative organisms ({link]). Up to 90 percent of the cell-wall in 
Gram-positive bacteria is composed of peptidoglycan, and most of the rest 
is composed of acidic substances called teichoic acids. Teichoic acids may 
be covalently linked to lipids in the plasma membrane to form lipoteichoic 
acids. Lipoteichoic acids anchor the cell wall to the cell membrane. Gram- 
negative bacteria have a relatively thin cell wall composed of a few layers 
of peptidoglycan (only 10 percent of the total cell wall), surrounded by an 
outer envelope containing lipopolysaccharides (LPS) and lipoproteins. This 
outer envelope is sometimes referred to as a second lipid bilayer. The 
chemistry of this outer envelope is very different, however, from that of the 
typical lipid bilayer that forms plasma membranes. 


Note: 


Visual Connection 


poteichoic acid —_ Lipopolysaccharide Porin 


Lipoprotein 
Outer 
Peptidoglycan #\ membrane 
cell wal Periplasmic 
space 
L ene Inner 
L sane membrane 
Gram-positive bacteria Gram-negative bacteria 


Cell walls in Gram-positive and Gram-negative bacteria. 
Bacteria are divided into two major groups: Gram positive and 
Gram negative. Both groups have a cell wall composed of 
peptidoglycan: in Gram-positive bacteria, the wall is thick, 
whereas in Gram-negative bacteria, the wall is thin. In Gram- 
negative bacteria, the cell wall is surrounded by an outer 
membrane that contains lipopolysaccharides and lipoproteins. 
Porins are proteins in this cell membrane that allow substances 
to pass through the outer membrane of Gram-negative bacteria. 


In Gram-positive bacteria, lipoteichoic acid anchors the cell 
wall to the cell membrane. (credit: modification of work by 
"Franciscosp2"/Wikimedia Commons) 


Which of the following statements is true? 


a. Gram-positive bacteria have a single cell wall anchored to the cell 
membrane by lipoteichoic acid. 

b. Porins allow entry of substances into both Gram-positive and Gram- 
negative bacteria. 

c. The cell wall of Gram-negative bacteria is thick, and the cell wall of 
Gram-positive bacteria is thin. 

d. Gram-negative bacteria have a cell wall made of peptidoglycan, 
whereas Gram-positive bacteria have a cell wall made of lipoteichoic 
acid. 


Archaean cell walls do not have peptidoglycan. There are four different 
types of archaean cell walls. One type is composed of 
pseudopeptidoglycan, which is similar to peptidoglycan in morphology but 
contains different sugars in the polysaccharide chain. The other three types 
of cell walls are composed of polysaccharides, glycoproteins, or pure 
protein. Other differences between Bacteria and Archaea are seen in [link]. 
Note that features related to DNA replication, transcription and translation 
in Archaea are similar to those seen in eukaryotes. 


Differences and Similarities between Bacteria and Archaea 


Baffestencds and Similarities between Bacteria and Archaea 


Characteristic 


Structural 
Characteristic 


Cell type 


Cell morphology 


Cell wall 


Cell membrane 
type 


Plasma membrane 
lipids 


Chromosome 


Replication 
origins 


RNA polymerase 


Initiator tRNA 


Streptomycin 
inhibition 


Calvin cycle 


Bacteria 


Bacteria 
Prokaryotic 
Variable 


Contains 
peptidoglycan 


Lipid bilayer 


Fatty acids- 
glycerol ester 


Typically circular 


Single 


Single 


Formyl- 
methionine 


Sensitive 


Yes 


Archaea 


Archaea 
Prokaryotic 
Variable 


Does not contain 
peptidoglycan 


Lipid bilayer or lipid 
monolayer 


Phytanyl-glycerol 
ethers 


Typically circular 


Multiple 


Multiple 


Methionine 


Resistant 


No 


Reproduction 


Reproduction in prokaryotes is asexual and usually takes place by binary 
fission. (Recall that the DNA of a prokaryote is a single, circular 
chromosome.) Prokaryotes do not undergo mitosis; instead, the 
chromosome is replicated and the two resulting copies separate from one 
another, due to the growth of the cell. The prokaryote, now enlarged, is 
pinched inward at its equator and the two resulting cells, which are clones, 
separate. Binary fission does not provide an opportunity for genetic 
recombination or genetic diversity, but prokaryotes can share genes by three 
other mechanisms. 


In transformation, the prokaryote takes in DNA shed by other prokaryotes 
into its environment. If a nonpathogenic bacterium takes up DNA for a 
toxin gene from a pathogen and incorporates the new DNA into its own 
chromosome, it too may become pathogenic. In transduction, 
bacteriophages, the viruses that infect bacteria, may move short pieces of 
chromosomal DNA from one bacterium to another. Transduction results in 
a recombinant organism. Archaea also have viruses that may translocate 
genetic material from one individual to another. In conjugation, DNA is 
transferred from one prokaryote to another by means of a pilus, which 
brings the organisms into contact with one another, and provides a channel 
for transfer of DNA. The DNA transferred can be in the form of a plasmid 
or as a composite molecule, containing both plasmid and chromosomal 
DNA. These three processes of DNA exchange are shown in [link]. 


Reproduction can be very rapid: a few minutes for some species. This short 
generation time coupled with mechanisms of genetic recombination and 
high rates of mutation result in the rapid evolution of prokaryotes, allowing 
them to respond to environmental changes (such as the introduction of an 
antibiotic) very quickly. 


Pop 
BB 


(a) Transformation (b) Transduction (c) Conjugation 


Gene transfer mechanisms in prokaryotes. There are three mechanisms 
by which prokaryotes can exchange DNA. In (a) transformation, the 
cell takes up prokaryotic DNA directly from the environment. The 
DNA may remain separate as plasmid DNA or be incorporated into the 
host genome. In (b) transduction, a bacteriophage injects DNA into the 
cell that contains a small fragment of DNA from a different 
prokaryote. In (c) conjugation, DNA is transferred from one cell to 
another via a mating bridge, or pilus, that connects the two cells after 
the sex pilus draws the two bacteria close enough to form the bridge. 


Note: 

Evolution Connection 

The Evolution of Prokaryotes 

How do scientists answer questions about the evolution of prokaryotes? 
Unlike with animals, artifacts in the fossil record of prokaryotes offer very 
little information. Fossils of ancient prokaryotes look like tiny bubbles in 
rock. Some scientists turn to genetics and to the principle of the molecular 
clock, which holds that the more recently two species have diverged, the 
more similar their genes (and thus proteins) will be. Conversely, species 
that diverged long ago will have more genes that are dissimilar. 


Scientists at the NASA Astrobiology Institute and at the European 
Molecular Biology Laboratory collaborated to analyze the molecular 
evolution of 32 specific proteins common to 72 species of prokaryotes. 
[footnote] The model they derived from their data indicates that three 
important groups of bacteria—Actinobacteria, Deinococcus, and 
Cyanobacteria (collectively called Terrabacteria by the authors)—were the 
first to colonize land. Actinobacteria are a group of very common Gram- 
positive bacteria that produce branched structures like fungal mycelia, and 
include species important in decomposition of organic wastes. You will 
recall that Deinococcus is a genus of bacterium that is highly resistant to 
ionizing radiation. It has a thick peptidoglycan layer in addition to a second 
external membrane, so it has features of both Gram-positive and Gram- 
negative bacteria. 

Battistuzzi, FU, Feijao, A, and Hedges, SB. A genomic timescale of 
prokaryote evolution: Insights into the origin of methanogenesis, 
phototrophy, and the colonization of land. BioMed Central: Evolutionary 
Biology 4 (2004): 44, doi:10.1186/1471-2148-4-44. 

Cyanobacteria are photosynthesizers, and were probably responsible for 
the production of oxygen on the ancient earth. The timelines of divergence 
suggest that bacteria (members of the domain Bacteria) diverged from 
common ancestral species between 2.5 and 3.2 billion years ago, whereas 
the Archaea diverged earlier: between 3.1 and 4.1 billion years ago. 
Eukarya later diverged from the archaean line. The work further suggests 
that stromatolites that formed prior to the advent of cyanobacteria (about 
2.6 billion years ago) photosynthesized in an anoxic environment and that 
because of the modifications of the Terrabacteria for land (resistance to 
drying and the possession of compounds that protect the organism from 
excess light), photosynthesis using oxygen may be closely linked to 
adaptations to survive on land. 


Prokaryotic diversity 


Introduction 

"Perhaps bacteria may tentatively be regarded as biochemical experiments; 
owing to their relatively small size and rapid growth, variations must arise 
much more frequently than in more differentiated forms of life, and they 
can in addition afford to occupy more precarious positions in natural 
economy than larger organisms with more exacting requirements." Marjory 
Stephenson, in Bacterial Metabolism, (1930) 


Prokaryotic Diversity 


Prokaryotes are ubiquitous, and, as mentioned above, highly diverse in their 
metabolic activities. They cover every imaginable surface where there is 
sufficient moisture, and they live on and inside of other living things. In the 
typical human body, prokaryotic cells outnumber human body cells by 
about ten to one. They comprise the majority of living things in all 
ecosystems. Some prokaryotes thrive in environments that are inhospitable 
for most living things. Prokaryotes recycle nutrients—essential substances 
(such as carbon and nitrogen)—and they drive the evolution of new 
ecosystems, some of which are natural and others man-made. Prokaryotes 
have been on Earth since long before multicellular life appeared. 


Prokaryotes, the First Inhabitants of Earth 


When and where did life begin? What were the conditions on Earth when 
life began? Prokaryotes were the first forms of life on Earth, and they 
existed for billions of years before plants and animals appeared. The Earth 
and its moon are thought to be about 4.54 billion years old. This estimate is 
based on evidence from radiometric dating of meteorite material together 
with other substrate material from Earth and the moon. Early Earth had a 
very different atmosphere (contained less molecular oxygen) than it does 
today and was subjected to strong radiation; thus, the first organisms would 
have flourished where they were more protected, such as in ocean depths or 
beneath the surface of the Earth. At this time too, strong volcanic activity 
was common on Earth, so it is likely that these first organisms—the first 
prokaryotes—were adapted to very high temperatures. Early Earth was 


prone to geological upheaval and volcanic eruption, and was subject to 
bombardment by mutagenic radiation from the sun. The first organisms 
were prokaryotes that could withstand these harsh conditions. 


Microbial Mats 


Microbial mats or large biofilms may represent the earliest forms of life on 
Earth; there is fossil evidence of their presence starting about 3.5 billion 
years ago. A microbial mat is a multi-layered sheet of prokaryotes ((link]) 
that includes mostly bacteria, but also archaea. Microbial mats are a few 
centimeters thick, and they typically grow where different types of 
materials interface, mostly on moist surfaces. The various types of 
prokaryotes that comprise them carry out different metabolic pathways, and 
that is the reason for their various colors. Prokaryotes in a microbial mat are 
held together by a glue-like sticky substance that they secrete called 
extracellular matrix. 


The first microbial mats likely obtained their energy from chemicals found 
near hydrothermal vents. A hydrothermal vent is a breakage or fissure in 
the Earth’s surface that releases geothermally heated water. With the 
evolution of photosynthesis about 3 billion years ago, some prokaryotes in 
microbial mats came to use a more widely available energy source— 
sunlight—whereas others were still dependent on chemicals from 
hydrothermal vents for energy and food. 


This (a) microbial mat, about one meter in 


diameter, grows over a hydrothermal vent in 
the Pacific Ocean in a region known as the 
“Pacific Ring of Fire.” The mat helps retain 
microbial nutrients. Chimneys such as the 
one indicated by the arrow allow gases to 
escape. (b) In this micrograph, bacteria are 
visualized using fluorescence microscopy. 
(credit a: modification of work by Dr. Bob 
Embley, NOAA PMEL, Chief Scientist; 
credit b: modification of work by Ricardo 
Murga, Rodney Donlan, CDC; scale-bar 
data from Matt Russell) 


Stromatolites 


Fossilized microbial mats represent the earliest record of life on Earth. A 
stromatolite is a sedimentary structure formed when minerals precipitate 
out of water by prokaryotes in a microbial mat ({link]). Stromatolites form 
layered rocks made of carbonate or silicate. Although most stromatolites are 
artifacts from the past, there are places on Earth where stromatolites are still 
forming. For example, growing stromatolites have been found in the Anza- 
Borrego Desert State Park in San Diego County, California. 


(a) These living stromatolites are located in Shark 


Bay, Australia. (b) These fossilized stromatolites, 
found in Glacier National Park, Montana, are 
nearly 1.5 billion years old. (credit a: Robert 

Young; credit b: P. Carrara, NPS) 


The Ancient Atmosphere 


Evidence indicates that during the first two billion years of Earth’s 
existence, the atmosphere was anoxic, meaning that there was no molecular 
oxygen. Therefore, only those organisms that can grow without oxygen— 
anaerobic organisms—were able to live. Autotrophic organisms that 
convert solar energy into chemical energy are called phototrophs, and they 
appeared within one billion years of the formation of Earth. Then, 
cyanobacteria, also known as blue-green algae, evolved from these simple 
phototrophs one billion years later. Cyanobacteria ((link]) began the 
oxygenation of the atmosphere. Increased atmospheric oxygen allowed the 
development of more efficient O5-utilizing catabolic pathways. It also 
opened up the land to increased colonization, because some O, is converted 
into O3 (ozone) and ozone effectively absorbs the ultraviolet light that 
would otherwise cause lethal mutations in DNA. Ultimately, the increase in 
O» concentrations allowed the evolution of other life forms. 


This hot spring in Yellowstone 
National Park flows toward the 
foreground. Cyanobacteria in 
the spring are green, and as 
water flows down the gradient, 
the intensity of the color 
increases as cell density 
increases. The water is cooler at 
the edges of the stream than in 
the center, causing the edges to 
appear greener. (credit: Graciela 
Brelles-Marino) 


Microbes Are Adaptable: Life in Moderate and Extreme 
Environments 


Some organisms have developed strategies that allow them to survive harsh 
conditions. Prokaryotes thrive in a vast array of environments: Some grow 
in conditions that would seem very normal to us, whereas others are able to 
thrive and grow under conditions that would kill a plant or animal. Almost 
all prokaryotes have a cell wall, a protective structure that allows them to 
survive in both hyper- and hypo-osmotic conditions. Some soil bacteria are 
able to form endospores that resist heat and drought, thereby allowing the 
organism to survive until favorable conditions recur. These adaptations, 
along with others, allow bacteria to be the most abundant life form in all 
terrestrial and aquatic ecosystems. 


Other bacteria and archaea are adapted to grow under extreme conditions 
and are called extremophiles, meaning “lovers of extremes.” 
Extremophiles have been found in all kinds of environments: the depth of 
the oceans, hot springs, the Artic and the Antarctic, in very dry places, deep 
inside Earth, in harsh chemical environments, and in high radiation 
environments ({link]), just to mention a few. These organisms give us a 
better understanding of prokaryotic diversity and open up the possibility of 


finding new prokaryotic species that may lead to the discovery of new 
therapeutic drugs or have industrial applications. Because they have 
specialized adaptations that allow them to live in extreme conditions, many 
extremophiles cannot survive in moderate environments. There are many 
different groups of extremophiles: They are identified based on the 
conditions in which they grow best, and several habitats are extreme in 
multiple ways. For example, a soda lake is both salty and alkaline, so 
organisms that live in a soda lake must be both alkaliphiles and halophiles 
({link]). Other extremophiles, like radioresistant organisms, do not prefer 
an extreme environment (in this case, one with high levels of radiation), but 
have adapted to survive in it ({link]). 


Extremophiles and Their Preferred Conditions 


Extremophile Type Conditions for Optimal Growth 
Acidophiles pH 3 or below 

Alkaliphiles pH 9 or above 

Thermophiles Temperature 60—80 °C (140-176 °F) 
Hyperthermophiles Temperature 80—122 °C (176-250 °F) 
Psychrophiles Temperature of -15 °C (5 °F) or lower 
Halophiles Salt concentration of at least 0.2 M 


Osmophiles High sugar concentration 


Deinococcus 
radiodurans, visualized 
in this false color 
transmission electron 
micrograph, is a 
prokaryote that can 
tolerate very high doses 
of ionizing radiation. It 
has developed DNA 
repair mechanisms that 
allow it to reconstruct its 
chromosome even if it 
has been broken into 
hundreds of pieces by 
radiation or heat. (credit: 
modification of work by 
Michael Daly; scale-bar 
data from Matt Russell) 


The Ecology of Biofilms 


Until a couple of decades ago, microbiologists used to think of prokaryotes 
as isolated entities living apart. This model, however, does not reflect the 
true ecology of prokaryotes, most of which prefer to live in communities 
where they can interact. A biofilm is a microbial community (({link]) held 
together in a gummy-textured matrix that consists primarily of 
polysaccharides secreted by the organisms, together with some proteins and 
nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied 
biofilms are composed of prokaryotes, although fungal biofilms have also 
been described as well as some composed of a mixture of fungi and 
bacteria. 


Biofilms are present almost everywhere: they can cause the clogging of 
pipes and readily colonize surfaces in industrial settings. In recent, large- 
scale outbreaks of bacterial contamination of food, biofilms have played a 
major role. They also colonize household surfaces, such as kitchen 
counters, cutting boards, sinks, and toilets, as well as places on the human 
body, such as the surfaces of our teeth. 


Interactions among the organisms that populate a biofilm, together with 
their protective exopolysaccharidic (EPS) environment, make these 
communities more robust than free-living, or planktonic, prokaryotes. The 
sticky substance that holds bacteria together also excludes most antibiotics 
and disinfectants, making biofilm bacteria hardier than their planktonic 
counterparts. Overall, biofilms are very difficult to destroy because they are 
resistant to many common forms of sterilization. 


Note: 


Five stages of biofilm development 
are shown. During stage 1, initial 
attachment, bacteria adhere to a solid 
surface via weak van der Waals 
interactions. During stage 2, 
irreversible attachment, hairlike 
appendages called pili permanently 
anchor the bacteria to the surface. 
During stage 3, maturation I, the 
biofilm grows through cell division 
and recruitment of other bacteria. An 
extracellular matrix composed 
primarily of polysaccharides holds the 
biofilm together. During stage 4, 
maturation II, the biofilm continues to 
grow and takes on a more complex 
shape. During stage 5, dispersal, the 
biofilm matrix is partly broken down, 
allowing some bacteria to escape and 
colonize another surface. Micrographs 
of a Pseudomonas aeruginosa biofilm 
in each of the stages of development 
are shown. (credit: D. Davis, Don 
Monroe, PLoS) 


Bacterial Diseases in Humans 


Devastating pathogen-borne diseases and plagues, both viral and bacterial 
in nature, have affected humans since the beginning of human history. The 
true cause of these diseases was not understood at the time, and some 
people thought that diseases were a spiritual punishment. Over time, people 
came to realize that staying apart from afflicted persons, and disposing of 
the corpses and personal belongings of victims of illness, reduced their own 
chances of getting sick. [link] below lists the disease and known associated 
bacterial cause. 


Disease Bacterium 

Anthrax Bacillus anthracis 

Botulism Clostridium botulinum 
Chlamydia Chlamydia trachomatis 
Plague Yersinia pestis 

Tuberculosis Mycobacterium tuberculosis 
Peptic ulcers Helicobacter pylori 

Cholera Vibrio cholerae 

Lyme disease Borrelia burgdorferi 


Human Disease and associated bacterium 


Epidemiologists study how diseases affect a population. An epidemic is a 
disease that occurs in an unusually high number of individuals in a 
population at the same time. A pandemic is a widespread, usually 
worldwide, epidemic. An endemic disease is a disease that is constantly 
present, usually at low incidence, in a population. 


Long History of Bacterial Disease 


There are records about infectious diseases as far back as 3000 B.C. A 
number of significant pandemics caused by bacteria have been documented 
over several hundred years. Some of the most memorable pandemics led to 
the decline of cities and nations. 


In the 21°' century, infectious diseases remain among the leading causes of 
death worldwide, despite advances made in medical research and treatments 
in recent decades. A disease spreads when the pathogen that causes it is 
passed from one person to another. For a pathogen to cause disease, it must 
be able to reproduce in the host’s body and damage the host in some way. 


The Plague of Athens 


In 430 B.C., the Plague of Athens killed one-quarter of the Athenian troops 
that were fighting in the great Peloponnesian War and weakened Athens’ 
dominance and power. The plague impacted people living in overcrowded 
Athens as well as troops aboard ships that had to return to Athens. The 
source of the plague may have been identified recently when researchers 
from the University of Athens were able to use DNA from teeth recovered 
from a mass grave. The scientists identified nucleotide sequences from a 
pathogenic bacterium, Salmonella enterica serovar Typhi ({link]), which 
causes typhoid fever, !2o™2te] This disease is commonly seen in 
overcrowded areas and has caused epidemics throughout recorded history. 
Papagrigorakis MJ, Synodinos PN, and Yapijakis C. Ancient typhoid 
epidemic reveals possible ancestral strain of Salmonella enterica serovar 
Typhi. Infect Genet Evol 7 (2007): 126—7, Epub 2006 Jun. 


Salmonella enterica serovar 
Typhi, the causative agent of 
Typhoid fever, is a Gram-negative, 
rod-shaped gamma 
protobacterium. Typhoid fever, 
which is spread through feces, 
causes intestinal hemorrhage, high 
fever, delirium and dehydration. 
Today, between 16 and 33 million 
cases of this re-emerging disease 
occur annually, resulting in over 
200,000 deaths. Carriers of the 
disease can be asymptomatic. In a 
famous case in the early 1900s, a 
cook named Mary Mallon 
unknowingly spread the disease to 
over fifty people, three of whom 
died. Other Salmonella serotypes 
cause food poisoning. (credit: 
modification of work by NCI, 
CDC) 


Bubonic Plagues 


From 541 to 750, an outbreak of what was likely a bubonic plague (the 
Plague of Justinian), eliminated one-quarter to one-half of the human 
population in the eastern Mediterranean region. The population in Europe 
dropped by 50 percent during this outbreak. Bubonic plague would strike 
Europe more than once. 


One of the most devastating pandemics was the Black Death (1346 to 
1361) that is believed to have been another outbreak of bubonic plague 
caused by the bacterium Yersinia pestis. It is thought to have been 
contracted initially in China and spread along the Silk Road, a network of 
land and sea trade routes, to the Mediterranean region and Europe, carried 
by rat fleas living on black rats that were always present on ships. The 
Black Death reduced the world’s population from an estimated 450 million 
to about 350 to 375 million. Bubonic plague struck London hard again in 
the mid-1600s ({link]). In modern times, approximately 1,000 to 3,000 
cases of plague arise globally each year. Although contracting bubonic 
plague before antibiotics meant almost certain death, the bacterium 
responds to several types of modern antibiotics, and mortality rates from 
plague are now very low. 


The (a) Great Plague of London killed an 
estimated 200,000 people, or about twenty percent 
of the city’s population. The causative agent, the 
(b) bacterium Yersinia pestis, is a Gram-negative, 
rod-shaped bacterium from the class Gamma 
Proteobacteria. The disease is transmitted through 
the bite of an infected flea, which is infected by a 


rodent. Symptoms include swollen lymph nodes, 
fever, seizure, vomiting of blood, and (c) 
gangrene. (credit b: Rocky Mountain 
Laboratories, NIAID, NIH; scale-bar data from 
Matt Russell; credit c: Textbook of Military 
Medicine, Washington, D.C., U.S. Dept. of the 
Army, Office of the Surgeon General, Borden 
Institute) 


Migration of Diseases to New Populations 


Over the centuries, Europeans tended to develop genetic immunity to 
endemic infectious diseases, but when European conquerors reached the 
western hemisphere, they brought with them disease-causing bacteria and 
viruses, which triggered epidemics that completely devastated populations 
of Native Americans, who had no natural resistance to many European 
diseases. It has been estimated that up to 90 percent of Native Americans 
died from infectious diseases after the arrival of Europeans, making 
conquest of the New World a foregone conclusion. 


Emerging and Re-emerging Diseases 


The distribution of a particular disease is dynamic. Therefore, changes in 
the environment, the pathogen, or the host population can dramatically 
impact the spread of a disease. According to the World Health Organization 
(WHO) an emerging disease ([link]) is one that has appeared in a 
population for the first time, or that may have existed previously but is 
rapidly increasing in incidence or geographic range. This definition also 
includes re-emerging diseases that were previously under control. 
Approximately 75 percent of recently emerging infectious diseases 
affecting humans are zoonotic diseases, zoonoses, diseases that primarily 
infect animals and are transmitted to humans; some are of viral origin and 
some are of bacterial origin. Brucellosis is an example of a prokaryotic 


zoonosis that is re-emerging in some regions, and necrotizing fasciitis 
(commonly known as flesh-eating bacteria) has been increasing in virulence 
for the last 80 years for unknown reasons. 


Vancomycin-resistant Multidrug-resistant 
Staphylococcus aureus tuberculosis 


The map shows regions where bacterial 
diseases are emerging or reemerging. (credit: 
modification of work by NIH) 


Some of the present emerging diseases are not actually new, but are 
diseases that were catastrophic in the past ([link]). They devastated 
populations and became dormant for a while, just to come back, sometimes 
more virulent than before, as was the case with bubonic plague. Other 
diseases, like tuberculosis, were never eradicated but were under control in 
some regions of the world until coming back, mostly in urban centers with 
high concentrations of immunocompromised people. The WHO has 
identified certain diseases whose worldwide re-emergence should be 
monitored. Among these are two viral diseases (dengue fever and yellow 
fever), and three prokaryotic diseases (diphtheria, cholera, and bubonic 
plague). The war against infectious diseases has no foreseeable end. 


Life Cycle of the Ixodes scapularis Tick 


0 reeds once, Yy 
(Deer is preferred host) 2 
Spring 3 weeks i ¢ {\ o Fall 


IN 
Nymph Yer Deposited 
Egg. © —@aduts die 


Feeds once, 3-4 days ff 
1 month (Mouse is preferred host) 


Larvae 
w Feeds once, 2 days 
{iilouse is preferred host) 


Summer 


(a) (c) 


Lyme disease often, but not always, results in (a) a 
characteristic bullseye rash. The disease is caused 
by a (b) Gram-negative spirochete bacterium of 
the genus Borellia. The bacteria (c) infect ticks, 
which in turns infect mice. Deer are the preferred 
secondary host, but the ticks also may feed on 
humans. Untreated, the disease causes chronic 
disorders in the nervous system, eyes, joints, and 
heart. The disease is named after Lyme, 
Connecticut, where an outbreak occurred in 1995 
and has subsequently spread. The disease is not 
new, however. Genetic evidence suggests that Otzi 
the Iceman, a 5,300-year-old mummy found in the 
Alps, was infected with Borellia. (credit a: James 
Gathany, CDC; credit b: CDC; scale-bar data from 
Matt Russell) 


Biofilms and Disease 


Recall that biofilms are microbial communities that are very difficult to 
destroy. They are responsible for diseases such as infections in patients with 
cystic fibrosis, Legionnaires’ disease, and otitis media. They produce dental 
plaque and colonize catheters, prostheses, transcutaneous and orthopedic 
devices, contact lenses, and internal devices such as pacemakers. They also 
form in open wounds and burned tissue. In healthcare environments, 


biofilms grow on hemodialysis machines, mechanical ventilators, shunts, 
and other medical equipment. In fact, 65 percent of all infections acquired 
in the hospital (nosocomial infections) are attributed to biofilms. Biofilms 
are also related to diseases contracted from food because they colonize the 
surfaces of vegetable leaves and meat, as well as food-processing 
equipment that isn’t adequately cleaned. 


Biofilm infections develop gradually; sometimes, they do not cause 
symptoms immediately. They are rarely resolved by host defense 
mechanisms. Once an infection by a biofilm is established, it is very 
difficult to eradicate, because biofilms tend to be resistant to most of the 
methods used to control microbial growth, including antibiotics. Biofilms 
respond poorly or only temporarily to antibiotics; it has been said that they 
can resist up to 1,000 times the antibiotic concentrations used to kill the 
same bacteria when they are free-living or planktonic. An antibiotic dose 
that large would harm the patient; therefore, scientists are working on new 
ways to get rid of biofilms. 


Antibiotics: Are We Facing a Crisis? 


The word antibiotic comes from the Greek anti meaning “against” and bios 
meaning “life.” An antibiotic is a chemical, produced either by microbes or 
synthetically, that is hostile to the growth of other organisms. Today’s news 
and media often address concerns about an antibiotic crisis. Are the 
antibiotics that easily treated bacterial infections in the past becoming 
obsolete? Are there new “superbugs”—bacteria that have evolved to 
become more resistant to our arsenal of antibiotics? Is this the beginning of 
the end of antibiotics? All these questions challenge the healthcare 
community. 


One of the main causes of resistant bacteria is the abuse of antibiotics. The 
imprudent and excessive use of antibiotics has resulted in the natural 
selection of resistant forms of bacteria. The antibiotic kills most of the 
infecting bacteria, and therefore only the resistant forms remain. These 
resistant forms reproduce, resulting in an increase in the proportion of 
resistant forms over non-resistant ones. Another major misuse of antibiotics 
is in patients with colds or the flu, for which antibiotics are useless. Another 


problem is the excessive use of antibiotics in livestock. The routine use of 
antibiotics in animal feed promotes bacterial resistance as well. In the 
United States, 70 percent of the antibiotics produced are fed to animals. 
These antibiotics are given to livestock in low doses, which maximize the 
probability of resistance developing, and these resistant bacteria are readily 
transferred to humans. 


One of the Superbugs: MRSA 


The imprudent use of antibiotics has paved the way for bacteria to expand 
populations of resistant forms. For example, Staphylococcus aureus, often 
called “staph,” is a common bacterium that can live in the human body and 
is usually easily treated with antibiotics. A very dangerous strain, however, 
methicillin-resistant Staphylococcus aureus (MRSA) has made the news 
over the past few years ((link]). This strain is resistant to many commonly 
used antibiotics, including methicillin, amoxicillin, penicillin, and oxacillin. 
MRSA can cause infections of the skin, but it can also infect the 
bloodstream, lungs, urinary tract, or sites of injury. While MRSA infections 
are common among people in healthcare facilities, they have also appeared 
in healthy people who haven’t been hospitalized but who live or work in 
tight populations (like military personnel and prisoners). Researchers have 
expressed concern about the way this latter source of MRSA targets a much 
younger population than those residing in care facilities. The Journal of the 
American Medical Association reported that, among MRSA-afflicted 
persons in healthcare facilities, the average age is 68, whereas people with 
“community-associated MRSA” (CA-MRSA) have an average age of 23. 
[footnote] 

Naimi, TS, LeDell, KH, Como-Sabetti, K, et al. Comparison of community- 
and health care-associated methicillin-resistant Staphylococcus aureus 
infection. JAMA 290 (2003): 2976-84, doi: 10.1001/jama.290.22.2976. 


This scanning electron 
micrograph shows methicillin- 
resistant Staphylococcus aureus 
bacteria, commonly known as 
MRSA. S. Aureus is not always 
pathogenic, but can cause 
diseases such as food poisoning 
and skin and respiratory 
infections. (credit: modification 
of work by Janice Haney Carr; 
scale-bar data from Matt 
Russell) 


In summary, the medical community is facing an antibiotic crisis. Some 
scientists believe that after years of being protected from bacterial 
infections by antibiotics, we may be returning to a time in which a simple 
bacterial infection could again devastate the human population. Researchers 
are developing new antibiotics, but it takes many years to of research and 
clinical trials, plus financial investments in the millions of dollars, to 
generate an effective and approved drug. 


Foodborne Diseases 


Prokaryotes are everywhere: They readily colonize the surface of any type 
of material, and food is not an exception. Most of the time, prokaryotes 


colonize food and food-processing equipment in the form of a biofilm. 
Outbreaks of bacterial infection related to food consumption are common. 
A foodborne disease (colloquially called “food poisoning”) is an illness 
resulting from the consumption of contaminated food, or the pathogenic 
bacteria, viruses, or other parasites that contaminate food. Although the 
United States has one of the safest food supplies in the world, the U.S. 
Centers for Disease Control and Prevention (CDC) has reported that “76 
million people get sick, more than 300,000 are hospitalized, and 5,000 
Americans die each year from foodborne illness.” 


The characteristics of foodborne illnesses have changed over time. In the 
past, it was relatively common to hear about sporadic cases of botulism, the 
potentially fatal disease produced by a toxin from the anaerobic bacterium 
Clostridium botulinum. Some of the most common sources for this 
bacterium were non-acidic canned foods, homemade pickles, and processed 
meat and sausages. The can, jar, or package created a suitable anaerobic 
environment where Clostridium could grow. Proper sterilization and 
canning procedures have reduced the incidence of this disease. 


While people may tend to think of foodborne illnesses as associated with 
animal-based foods, most cases are now linked to produce. There have been 
serious, produce-related outbreaks associated with raw spinach in the 
United States and with vegetable sprouts in Germany, and these types of 
outbreaks have become more common. The raw spinach outbreak in 2006 
was produced by the bacterium E. coli serotype O157:H7. A serotype is a 
strain of bacteria that carries a set of similar antigens on its cell surface, and 
there are often many different serotypes of a bacterial species. Most E. coli 
are not particularly dangerous to humans, but serotype 0157:H7 can cause 
bloody diarrhea and is potentially fatal. 


All types of food can potentially be contaminated with bacteria. Recent 
outbreaks of Salmonella reported by the CDC occurred in foods as diverse 
as peanut butter, alfalfa sprouts, and eggs. A deadly outbreak in Germany in 
2010 was caused by E. coli contamination of vegetable sprouts ({link]). The 
strain that caused the outbreak was found to be a new serotype not 
previously involved in other outbreaks, which indicates that E. coli is 
continuously evolving. 


(a) Vegetable sprouts grown at an organic farm were 
the cause of an (b) EF. coli outbreak that killed 32 
people and sickened 3,800 in Germany in 2011. The 
strain responsible, E. coli 0104:H4, produces Shiga 
toxin, a substance that inhibits protein synthesis in the 
host cell. The toxin (c) destroys red blood cells 
resulting in bloody diarrhea. Deformed red blood 
cells clog the capillaries of the kidney, which can lead 
to kidney failure, as happened to 845 patients in the 
2011 outbreak. Kidney failure is usually reversible, 
but some patients experience kidney problems years 
later. (credit c: NIDDK, NIH) 


Note: 

Career Connection 

Epidemiologist 

Epidemiology is the study of the occurrence, distribution, and determinants 
of health and disease in a population. It is, therefore, part of public health. 
An epidemiologist studies the frequency and distribution of diseases within 
human populations and environments. 

Epidemiologists collect data about a particular disease and track its spread 
to identify the original mode of transmission. They sometimes work in 
close collaboration with historians to try to understand the way a disease 
evolved geographically and over time, tracking the natural history of 
pathogens. They gather information from clinical records, patient 
interviews, surveillance, and any other available means. That information 


is used to develop strategies, such as vaccinations ([link]), and design 
public health policies to reduce the incidence of a disease or to prevent its 
spread. Epidemiologists also conduct rapid investigations in case of an 
outbreak to recommend immediate measures to control it. 

An epidemiologist has a bachelor’s degree, plus a master’s degree in public 
health (MPH). Many epidemiologists are also physicians (and have an 
M.D.), or they have a Ph.D. in an associated field, such as biology or 
microbiology. 


Vaccinations can slow the spread of 
communicable diseases. (credit: 
modification of work by Daniel 

Paquet) 


Beneficial Bacteria 


Not all prokaryotes are pathogenic. On the contrary, pathogens represent 
only a very small percentage of the diversity of the microbial world. In fact, 
our life would not be possible without prokaryotes. Just think about the role 
of prokaryotes in biogeochemical cycles. 


Cooperation between Bacteria and Eukaryotes: Nitrogen 
Fixation 


Nitrogen is a very important element to living things, because it is part of 
nucleotides and amino acids that are the building blocks of nucleic acids 
and proteins, respectively. Nitrogen is usually the most limiting element in 
terrestrial ecosystems, with atmospheric nitrogen, N>, providing the largest 
pool of available nitrogen. However, eukaryotes cannot use atmospheric, 
gaseous nitrogen to synthesize macromolecules. Fortunately, nitrogen can 
be “fixed,” meaning it is converted into ammonia (NH3) either biologically 
or abiotically. Abiotic nitrogen fixation occurs as a result of lightning or by 
industrial processes. 


Biological nitrogen fixation (BNF) is exclusively carried out by 
prokaryotes: soil bacteria, cyanobacteria, and Frankia spp. (filamentous 
bacteria interacting with actinorhizal plants such as alder, bayberry, and 
sweet fern). After photosynthesis, BNF is the second most important 
biological process on Earth. The equation representing the process is as 
follows 

Equation: 


N.+16ATP + 8e + 8H* — 2NH;+ 16ADP + 16Pi+ H, 


where Pi stands for inorganic phosphate. The total fixed nitrogen through 
BNF is about 100 to 180 million metric tons per year. Biological processes 
contribute 65 percent of the nitrogen used in agriculture. 


Cyanobacteria are the most important nitrogen fixers in aquatic 
environments. In soil, members of the genus Clostridium are examples of 
free-living, nitrogen-fixing bacteria. Other bacteria live symbiotically with 
legume plants, providing the most important source of BNF. Symbionts 
may fix more nitrogen in soils than free-living organisms by a factor of 10. 
Soil bacteria, collectively called rhizobia, are able to symbiotically interact 
with legumes to form nodules, specialized structures where nitrogen 
fixation occurs ({link]). Nitrogenase, the enzyme that fixes nitrogen, is 
inactivated by oxygen, so the nodule provides an oxygen-free area for 
nitrogen fixation to take place. This process provides a natural and 
inexpensive plant fertilizer, as it reduces atmospheric nitrogen into 
ammonia, which is easily usable by plants. The use of legumes is an 
excellent alternative to chemical fertilization and is of special interest to 


sustainable agriculture, which seeks to minimize the use of chemicals and 
conserve natural resources. Through symbiotic nitrogen fixation, the plant 
benefits from using an endless source of nitrogen: the atmosphere. Bacteria 
benefit from using photosynthates (carbohydrates produced during 
photosynthesis) from the plant and having a protected niche. Additionally, 
the soil benefits from being naturally fertilized. Therefore, the use of 
rhizobia as biofertilizers is a sustainable practice. 


Why are legumes so important? Some, like soybeans, are key sources of 
agricultural protein. Some of the most important grain legumes are soybean, 
peanuts, peas, chickpeas, and beans. Other legumes, such as alfalfa, are 
used to feed cattle. 


Soybean (Glycine max) is a 
legume that interacts 
symbiotically with the soil 
bacterium Bradyrhizobium 
japonicum to form specialized 
structures on the roots called 
nodules where nitrogen fixation 
occurs. (credit: USDA) 


Early Biotechnology: Cheese, Bread, Wine, Beer, and Yogurt 


According to the United Nations Convention on Biological Diversity, 
biotechnology is “any technological application that uses biological 
systems, living organisms, or derivatives thereof, to make or modify 
products or processes for specific use."!#22™°'e] The concept of “specific 
use” involves some sort of commercial application. Genetic engineering, 
artificial selection, antibiotic production, and cell culture are current topics 
of study in biotechnology. However, humans have used prokaryotes before 
the term biotechnology was even coined. In addition, some of the goods and 
services are as simple as cheese, bread, wine, beer, and yogurt, which 
employ both bacteria and other microbes, such as yeast, a fungus ([link]). 
http://www.cbd.int/convention/articles/?a=cbd-02, United Nations 
Convention on Biological Diversity: Article 2: Use of Terms. 


Some of the products derived from the use of 


prokaryotes in early biotechnology include (a) 
cheese, (b) wine, (c) beer and bread, and (d) yogurt. 
(credit bread: modification of work by F. 
Rodrigo/Wikimedia Commons; credit wine: 
modification of work by Jon Sullivan; credit beer 
and bread: modification of work by Kris Miller; 
credit yogurt: modification of work by Jon 
Sullivan) 


Cheese production began around 4,000—7,000 years ago when humans 
began to breed animals and process their milk. Fermentation in this case 
preserves nutrients: Milk will spoil relatively quickly, but when processed 
as cheese, it is more stable. As for beer, the oldest records of brewing are 
about 6,000 years old and refer to the Sumerians. Evidence indicates that 
the Sumerians discovered fermentation by chance. Wine has been produced 
for about 4,500 years, and evidence suggests that cultured milk products, 
like yogurt, have existed for at least 4,000 years. 


Using Prokaryotes to Clean up Our Planet: Bioremediation 


Microbial bioremediation is the use of prokaryotes (or microbial 
metabolism) to remove pollutants. Bioremediation has been used to remove 
agricultural chemicals (pesticides, fertilizers) that leach from soil into 
groundwater and the subsurface. Certain toxic metals and oxides, such as 
selenium and arsenic compounds, can also be removed from water by 
bioremediation. The reduction of SeO,°* to SeO3"2 and to Se® (metallic 
selenium) is a method used to remove selenium ions from water. Mercury is 
an example of a toxic metal that can be removed from an environment by 
bioremediation. As an active ingredient of some pesticides, mercury is used 
in industry and is also a by-product of certain processes, such as battery 
production. Methyl mercury is usually present in very low concentrations in 
natural environments, but it is highly toxic because it accumulates in living 
tissues. Several species of bacteria can carry out the biotransformation of 
toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas 
aeruginosa, can convert Hg*? into Hg®, which is nontoxic to humans. 


One of the most useful and interesting examples of the use of prokaryotes 
for bioremediation purposes is the cleanup of oil spills. The importance of 
prokaryotes to petroleum bioremediation has been demonstrated in several 
oil spills in recent years, such as the Exxon Valdez spill in Alaska (1989) 
({link]), the Prestige oil spill in Spain (2002), the spill into the 
Mediterranean from a Lebanon power plant (2006), and more recently, the 
BP oil spill in the Gulf of Mexico (2010). To clean up these spills, 
bioremediation is promoted by the addition of inorganic nutrients that help 
bacteria to grow. Hydrocarbon-degrading bacteria feed on hydrocarbons in 
the oil droplet, breaking down the hydrocarbons. Some species, such as 
Alcanivorax borkumensis, produce surfactants that solubilize the oil, 
whereas other bacteria degrade the oil into carbon dioxide. In the case of oil 
spills in the ocean, ongoing, natural bioremediation tends to occur, 
inasmuch as there are oil-consuming bacteria in the ocean prior to the spill. 
In addition to naturally occurring oil-degrading bacteria, humans select and 
engineer bacteria that possess the same capability with increased efficacy 
and spectrum of hydrocarbon compounds that can be processed. Under 
ideal conditions, it has been reported that up to 80 percent of the nonvolatile 
components in oil can be degraded within one year of the spill. Other oil 
fractions containing aromatic and highly branched hydrocarbon chains are 
more difficult to remove and remain in the environment for longer periods 
of time. 


(b) 


(a) Cleaning up oil after the Valdez spill in Alaska, 
workers hosed oil from beaches and then used a 
floating boom to corral the oil, which was finally 
skimmed from the water surface. Some species of 


bacteria are able to solubilize and degrade the oil. (b) 
One of the most catastrophic consequences of oil 
spills is the damage to fauna. (credit a: modification 
of work by NOAA; credit b: modification of work by 
GOLUBENKOV, NGO: Saving Taman) 


Note: 

Everyday Connection 

Microbes on the Human Body 

The commensal bacteria that inhabit our skin and gastrointestinal tract do a 
host of good things for us. They protect us from pathogens, help us digest 
our food, and produce some of our vitamins and other nutrients. These 
activities have been known for a long time. More recently, scientists have 
gathered evidence that these bacteria may also help regulate our moods, 
influence our activity levels, and even help control weight by affecting our 
food choices and absorption patterns. The Human Microbiome Project has 
begun the process of cataloging our normal bacteria (and archaea) so we 
can better understand these functions. 

A particularly fascinating example of our normal flora relates to our 
digestive systems. People who take high numbers of antibiotics tend to lose 
many of their normal gut bacteria, allowing a naturally antibiotic-resistant 
species called Clostridium difficile to overgrow and cause severe gastric 
problems, especially chronic diarrhea ([link]). Obviously, trying to treat 
this problem with antibiotics only makes it worse. However, it has been 
successfully treated by giving the patients fecal transplants from healthy 
donors to reestablish the normal intestinal microbial community. Clinical 
trials are underway to ensure the safety and effectiveness of this technique. 


This scanning electron micrograph 
shows Clostridium difficile, a 
Gram-positive, rod-shaped 
bacterium that causes severe 
diarrhea. Infection commonly 
occurs after the normal gut fauna is 
eradicated by antibiotics. (credit: 
modification of work by CDC, 
HHS; scale-bar data from Matt 
Russell) 


Scientists are also discovering that the absence of certain key microbes 
from our intestinal tract may set us up for a variety of problems. This 
seems to be particularly true regarding the appropriate functioning of the 
immune system. There are intriguing findings that suggest that the absence 
of these microbes is an important contributor to the development of 
allergies and some autoimmune disorders. Research is currently underway 
to test whether adding certain microbes to our internal ecosystem may help 
in the treatment of these problems as well as in treating some forms of 
autism. 


Kingdom Fungi 


Introduction 

"Now when you cut a forest, an ancient forest in particular, you are not just 
removing a lot of big trees and a few birds fluttering around in the canopy. 
You are drastically imperiling a vast array of species within a few square 
miles of you. The number of these species may go to tens of thousands. ... 
Many of them are still unknown to science, and science has not yet 
discovered the key role undoubtedly played in the maintenance of that 
ecosystem, as in the case of fungi, microorganisms, and many of the 
insects." Edward O. Wilson, "On Human Nature" (2000). In John H. 


Morgan, Naturally Good, (2005) 
- a 


(a) (b) (c) 


The (a) familiar mushroom is only one type of fungus. The 
brightly colored fruiting bodies of this (b) coral fungus are 
displayed. This (c) electron micrograph shows the spore- 
bearing structures of Aspergillus, a type of toxic fungi 
found mostly in soil and plants. (credit a: modification of 
work by Chris Wee; credit b: modification of work by Cory 
Zanker; credit c: modification of work by Janice Haney 
Carr, Robert Simmons, CDC; scale-bar data from Matt 
Russell) 


The word fungus comes from the Latin word for mushroom. Indeed, the 
familiar mushrooms are fungi, but there are many other types of fungi as 


well ((link]). The kingdom Fungi includes an enormous variety of living 
organisms collectively referred to as Eumycota, or true fungi. While 
scientists have identified about 100,000 species of fungi, this is only a 
fraction of the over 5 million species likely present on Earth. Edible 
mushrooms, yeasts, black mold, and Penicillium notatum (the producer of 
the antibiotic penicillin) are all members of the kingdom Fungi, which 
belongs to the domain Eukarya. As eukaryotes, a typical fungal cell 
contains a true nucleus and many membrane-bound organelles. 


Fungi were once considered plant-like organisms; however, DNA 
comparisons have shown that fungi are more closely related to animals than 
plants. Fungi are not capable of photosynthesis: They use complex organic 
compounds as sources of energy and carbon. Some fungal organisms 
multiply only asexually, whereas others undergo both asexual reproduction 
and sexual reproduction. Most fungi produce a large number of spores that 
are disseminated by the wind. Like bacteria, fungi play an essential role in 
ecosystems, because they are decomposers and participate in the cycling of 
nutrients by breaking down organic materials into simple molecules. 


Fungi often interact with other organisms, forming mutually beneficial or 
mutualistic associations. Fungi also cause serious infections in plants and 
animals. For example, Dutch elm disease is a particularly devastating 
fungal infection that destroys many native species of elm (Ulmus spp.). The 
fungus infects the vascular system of the tree. It was accidentally 
introduced to North America in the 1900s and decimated elm trees across 
the continent. Dutch elm disease is caused by the fungus Ophiostoma ulmi. 
The elm bark beetle acts as a vector and transmits the disease from tree to 
tree. Many European and Asiatic elms are less susceptible than American 
elms. 


In humans, fungal infections are generally considered challenging to treat 
because, unlike bacteria, they do not respond to traditional antibiotic 
therapy since they are also eukaryotes. These infections may prove deadly 
for individuals with a compromised immune system. 


Fungi have many commercial applications. The food industry uses yeasts in 
baking, brewing, and wine making. Many industrial compounds are 


byproducts of fungal fermentation. Fungi are the source of many 
commercial enzymes and antibiotics. 


Cell Structure and Function 


Fungi are eukaryotes and as such have a complex cellular organization. As 
eukaryotes, fungal cells contain a membrane-bound nucleus. A few types of 
fungi have structures comparable to the plasmids (loops of DNA) seen in 
bacteria. Fungal cells also contain mitochondria and a complex system of 
internal membranes, including the endoplasmic reticulum and Golgi 
apparatus. 


Fungal cells do not have chloroplasts. Although the photosynthetic pigment 
chlorophyll is absent, many fungi display bright colors, ranging from red to 
green to black. The poisonous Amanita muscaria (fly agaric) is 
recognizable by its bright red cap with white patches ([link]). Pigments in 
fungi are associated with the cell wall and play a protective role against 
ultraviolet radiation. Some pigments are toxic. 


The poisonous Amanita muscaria 
is native to the temperate and 
boreal regions of North America. 
(credit: Christine Majul) 


Like plant cells, fungal cells are surrounded by a thick cell wall; however, 
the rigid layers contain the complex polysaccharides chitin and glucan. 
Cellulose, the main component of plant cell walls, is found rarely in fungi. 
Chitin, also found in the exoskeleton of insects, gives structural strength to 
the cell walls of fungi. The cell wall protects the cell from desiccation and 
predators. Similar to plants, some fungi contain a large central vacuole. The 
large central vacuole permits growth without spending many resources on 
regenerating the expensive cytoplasm. Fungi have plasma membranes 
similar to other eukaryotes, except that the structure is stabilized by 
ergosterol, a steroid molecule that functions like the cholesterol found in 
animal plasma membranes. Most members of the kingdom Fungi are 
nonmotile. Flagella are produced only by the gametes in the primitive 
division Chytridiomycota. 


Growth 


The vegetative body of a fungus is called a thallus and can be unicellular or 
multicellular. Some fungi are dimorphic because they can go from being 
unicellular to multicellular depending on environmental conditions. 
Unicellular fungi are generally referred to as yeasts.Saccharomyces 
cerevisiae (baker’s yeast) and Candida species (the agents of thrush, a 
common fungal infection) are examples of unicellular fungi. 


Most fungi are multicellular organisms. They display two distinct 
morphological stages: vegetative and reproductive. The vegetative stage is 
characterized by a tangle of slender thread-like structures called hyphae 
(singular, hypha), whereas the reproductive stage can be more conspicuous. 
A mass of hyphae is called a mycelium ((link]). It can grow on a surface, in 
soil or decaying material, in a liquid, or even in or on living tissue. 
Although individual hypha must be observed under a microscope, the 
mycelium of a fungus can be very large with some species truly being “the 
fungus humongous.” The giant Armillaria ostoyae (honey mushroom) is 
considered the largest organism on Earth, spreading across over 2,000 acres 


of underground soil in eastern Oregon; it is estimated to be at least 2,400 
years old. 


The mycelium of the fungus 
Neotestudina rosati can be 


pathogenic to humans. The 
fungus enters through a cut or 
scrape and develops into a 
mycetoma, a chronic 
subcutaneous infection. (credit: 
CDG) 


Most fungal hyphae are divided into separate cells by end walls called septa 
(singular, septum. In most divisions (like plants, fungal phyla are called 
divisions by tradition) of fungi, tiny holes in the septa allow for the rapid 
flow of nutrients and small molecules from cell to cell along the hyphae. 
They are described as perforated septa. The hyphae in bread molds (which 
belong to the division Zygomycota) are not separated by septa. They are 
formed of large cells containing many nuclei, an arrangement described as 
coenocytic hyphae. 


Fungi thrive in environments that are moist and slightly acidic, and can 
grow with or without light. They vary in their oxygen requirements. Most 


fungi are obligate aerobes, requiring oxygen to survive. Other species, such 
as the Chytridiomycota that reside in the rumen of cattle, are obligate 
anaerobes, meaning that they cannot grow and reproduce in an environment 
with oxygen. Yeasts are facultative: They grow best in the presence of 
oxygen but can use fermentation in the absence of oxygen. The alcohol 
produced from yeast fermentation is used in wine and beer production, and 
the carbon dioxide they produce carbonates beer and sparkling wine, and 
makes bread rise. 


How Fungi Obtain Nutrition 


Like animals, fungi are heterotrophs: They use complex organic compounds 
as a source of carbon rather than fixing carbon dioxide from the 
atmosphere, as some bacteria and most plants do. In addition, fungi do not 
fix nitrogen from the atmosphere. Like animals, they must obtain it from 
their diet. However, unlike most animals that ingest food and then digest it 
internally in specialized organs, fungi perform these steps in the reverse 
order. Digestion precedes ingestion. First, exoenzymes, enzymes that 
catalyze reactions on compounds outside of the cell, are transported out of 
the hyphae where they break down nutrients in the environment. Then, the 
smaller molecules produced by the external digestion are absorbed through 
the large surface areas of the mycelium. As with animal cells, the fungal 
storage polysaccharide is glycogen rather than starch, as found in plants. 


Fungi are mostly saprobes, organisms that derive nutrients from decaying 
organic matter. They obtain their nutrients from dead or decomposing 
organic matter, mainly plant material. Fungal exoenzymes are able to break 
down insoluble polysaccharides, such as the cellulose and lignin of dead 
wood, into readily absorbable glucose molecules. Decomposers are 
important components of ecosystems, because they return nutrients locked 
in dead bodies to a form that is usable for other organisms. This role is 
discussed in more detail later. Because of their varied metabolic pathways, 
fungi fulfill an important ecological role and are being investigated as 
potential tools in bioremediation. For example, some species of fungi can 
be used to break down diesel oil and polycyclic aromatic hydrocarbons. 
Other species take up heavy metals such as cadmium and lead. 


Some fungi are parasitic and use enzymes systems similar to the ones 
described above to break down plant cell walls and access plant resources 
within the cell. Other parasitic fungi can also penetrate the outside defenses 
of animals and acquire nourishment from the organism. These fungi are 
pathogenic and cause disease in the host see the pathogenic section for 
more information. 


Reproduction 


Fungi reproduce sexually and/or asexually. When Fungi reproduce sexually, 
spores are produced by meiosis, and these spores are referred to as 
meiospores. Fungi can also produce spores mitosis (asexual reproduction), 
and the spores produced are called mitospores. There are groups of fungi 
that reproduce only using mitospores are called the mitosporic fungi. 


In both sexual and asexual reproduction, fungi produce spores that disperse 
from the parent organism by either floating on the wind or hitching a ride 
on an animal. Fungal spores are smaller and lighter than plant seeds. The 
giant puffball mushroom bursts open and releases trillions of spores. The 
huge number of spores released increases the likelihood of landing in an 
environment that will support growth ((Link]). 


(a) 


The (a) giant puff ball mushroom releases 
(b) a cloud of spores when it reaches 
maturity. (credit a: modification of work by 


Roger Griffith; credit b: modification of 
work by Pearson Scott Foresman, donated to 
the Wikimedia Foundation) 


Asexual Reproduction 


Fungi reproduce asexually by fragmentation of the mycelium. Fragments of 
hyphae can grow new colonies which are identical. The fragmentation of 
mycelium maintain clonal populations adapted to a specific niche, and 
allows for more rapid dispersal than sexual reproduction. 


The most common mode of asexual reproduction is through the formation 
of asexual spores or mitospores, which are produced by one parent only 
(through mitosis) and are genetically identical to that parent ({link]). Spores 
allow fungi to expand their distribution and colonize new environments. 
They may be released from the parent thallus either outside or within a 
specialized reproductive structure. 


Fungi Life Cycle 


Spores 


Germination Asevial Mitosis 


Reproduction 


Plasmogamy: Ket cs ee 
Haploid cells from = : ae ae 
two diffirent mycelia CFCe) A multi-cellular 
fuse to forma mycelium is formed. 


heterokaryotic cell 

with two or more 
: Sexual g 

lea in Reproduction fog Spores 
Heterokaryotic 
stage 


Karyogamy: Meiosis: 

The nuclei fuse to at, Haploid (1n) spores 
form a diploid (2n) are formed. 

zygote. 


Fungi may have both asexual and sexual stages 
of reproduction. 


There are many types of mitospores. Conidiospores are unicellular or 
multicellular spores that are released directly from the tip or side of the 
hypha. Other mitospores originate in the fragmentation of a hypha to form 
single cells that are released as spores; some of these have a thick wall 
surrounding the fragment. Yet others bud off the vegetative parent cell. 
Sporangiospores are produced in a sporangium ([link]). 


This bright field light micrograph shows 
the release of spores from a sporangium 
at the end of a hypha called a 
sporangiophore. The organism is a 
Mucor sp. fungus, a mold often found 
indoors. (credit: modification of work by 
Dr. Lucille Georg, CDC; scale-bar data 
from Matt Russell) 


Sexual Reproduction 


Sexual reproduction introduces genetic variation into a population of fungi. 
In fungi, sexual reproduction often occurs in response to adverse 
environmental conditions. During sexual reproduction, two mating types 
are produced. When both mating types are present in the same mycelium, it 
is called homothallic, or self-fertile. Heterothallic mycelia require two 
different, but compatible, mycelia to reproduce sexually. 


Although there are many variations in fungal sexual reproduction, all 
include the following three stages ({link]). First, during cytoplasmic fusion 
(plasmogamy), two haploid cells fuse, leading to a dikaryotic stage where 


two haploid nuclei coexist in a single cell. During karyogamy (“nuclear 
marriage”), the haploid nuclei fuse to form a diploid zygote nucleus. For 
some groups of fungi, karyogamy and plasmogamy can be separated for a 
long periods of time and some fungi maintain dikaryotic vegetative 
mycelium. Finally, meiosis takes place in the gametangia (singular, 
gametangium) organs, in which gametes of different mating types are 
generated. At this stage, spores are disseminated into the environment. 


Fungal Diversity 


The kingdom Fungi contains five major phyla that were established 
according to their mode of sexual reproduction or using molecular data. 
Polyphyletic, unrelated fungi that reproduce without a sexual cycle, are 
placed for convenience in a sixth group called a “form phylum”. Not all 
mycologists agree with this scheme. Rapid advances in molecular biology 
and the sequencing of rRNA genes continue to show new and different 
relationships between the various categories of fungi ([link]). The five true 
phyla of fungi are the Chytridiomycota (Chytrids), the Zygomycota 
(conjugated fungi), the Ascomycota (sac fungi), the Basidiomycota (club 
fungi) and the recently described Phylum Glomeromycota. The 
Deuteromycota is an informal group of unrelated fungi that all share a 
common character — they use strictly asexual reproduction or are called 
mitosporic. 


Se YX US ae 


Basidiomycota Ascomycota Glomeromycota Zygomycota Chytridiomycota Animalia 


A phylogenetic tree of five groups of fungi 
Chytridiomycota (Chytrids), the Zygomycota 
(conjugated fungi), the Ascomycota (sac fungi), the 
Basidiomycota (club fungi) and the recently described 
Phylum Glomeromycota. Work by Eva Horne. 


Note: “-mycota” is used to designate a phylum while “-mycetes” formally 
denotes a class or is used informally to refer to all members of the phylum. 


Chytridiomycota: The Chytrids 


The only class in the Phylum Chytridiomycota is the Chytridiomycetes. 
The chytrids are the simplest and most primitive Eumycota, or true fungi. 
The evolutionary record shows that the first recognizable chytrids appeared 
during the late pre-Cambrian period, more than 500 million years ago. Like 
all fungi, chytrids have chitin in their cell walls, but one group of chytrids 
has both cellulose and chitin in the cell wall. Most chytrids are unicellular; 
a few form multicellular organisms and hyphae, which have no septa 


between cells (coenocytic). They produce gametes and diploid zoospores 
that swim with the help of a single flagellum. 


The ecological habitat and cell structure of chytrids have much in common 
with protists. Chytrids usually live in aquatic environments, although some 
species live on land. Some species thrive as parasites on plants, insects, or 
amphibians ([link]), while others are saprobes. The chytrid species 
Allomyces is well characterized as an experimental organism. Its 
reproductive cycle includes both asexual and sexual phases. Allomyces 
produces diploid or haploid flagellated zoospores in a sporangium. 


The chytrid 
Batrachochytrium 
dendrobatidis is seen in these 
light micrographs as 


transparent spheres growing 
on (a) a freshwater arthropod 
and (b) algae. This chytrid 
causes skin diseases in many 
species of amphibians, 
resulting in species decline 
and extinction. (credit: 
modification of work by 
Johnson ML, Speare R., 
CDC) 


Zygomycota: The Conjugated Fungi 


The zygomycetes are a relatively small group of fungi belonging to the 
Phylum Zygomycota. They include the familiar bread mold, Rhizopus 
stolonifer, which rapidly propagates on the surfaces of breads, fruits, and 
vegetables. Most species are saprobes, living off decaying organic material; 
a few are parasites, particularly of insects. Zygomycetes play a considerable 
commercial role. The metabolic products of other species of Rhizopus are 
intermediates in the synthesis of semi-synthetic steroid hormones. 


Zygomycetes have a thallus of coenocytic hyphae in which the nuclei are 
haploid when the organism is in the vegetative stage. The fungi usually 
reproduce asexually by producing sporangiospores ([link]). The black tips 
of bread mold are the swollen sporangia packed with black spores ([link]). 
When spores land on a suitable substrate, they germinate and produce a new 
mycelium. Sexual reproduction starts when conditions become unfavorable. 
Two opposing mating strains (type + and type —) must be in close proximity 
for gametangia from the hyphae to be produced and fuse, leading to 
karyogamy. The developing diploid zygospores have thick coats that protect 
them from desiccation and other hazards. They may remain dormant until 
environmental conditions are favorable. When the zygospore germinates, it 
undergoes meiosis and produces haploid spores, which will, in turn, grow 
into a new organism. This form of sexual reproduction in fungi is called 


conjugation (although it differs markedly from conjugation in bacteria and 
protists), giving rise to the name “conjugated fungi”. 


Zygomycete Life Cycle 


Se 


Asexual 

Germination reproduction Mitosis 
Germination: 
Mycelia form. If the two mating 
types (+ and —) are in close 
proximity, extensions called 
gametangia form Se Germination 
between them. 

i ametangia 


Sporangium 
Mycelia (1n) 
(in) 


Plasmogamy: ~ Mating type Sexual 


Fusion between itt, Re 
+ and — mating 
types results ina Meiosis and 


zygosporangium germination: 
with multiple haploid A sporangium grows 
nuclei. The Zygosporangium on a short stalk. 


zygosporangium Haploid spores are 
forms a thick, Ome, = inside. 
protective 
coat. 

EL 


The nuclei fuse to 
form a zygote with 
multiple diploid nuclei. 


Zygomycetes have asexual and asexual life 
cycles. In the sexual life cycle, plus and minus 
mating types conjugate to form a 
zygosporangium. 


(a) (b) 


Sporangia grow at the end of stalks, which appear 
as (a) white fuzz seen on this bread mold, 
Rhizopus stolonifer. The (b) tips of bread mold are 
the spore-containing sporangia. (credit b: 
modification of work by "polandeze"/Flickr) 


Ascomycota: The Sac Fungi 


The majority of known fungi belong to the Phylum Ascomycota, which is 
characterized by the formation of an ascus (plural, asci), a sac-like structure 
that contains haploid ascospores. Many ascomycetes are of commercial 
importance. Some play a beneficial role, such as the yeasts used in baking, 
brewing, and wine fermentation, plus truffles and morels, which are held as 
gourmet delicacies. Aspergillus oryzae is used in the fermentation of rice to 
produce sake. Other ascomycetes parasitize plants and animals, including 
humans. For example, fungal pneumonia poses a significant threat to AIDS 
patients who have a compromised immune system. Ascomycetes not only 
infest and destroy crops directly; they also produce poisonous secondary 
metabolites that make crops unfit for consumption. Filamentous 
ascomycetes produce hyphae divided by perforated septa, allowing 
streaming of cytoplasm from one cell to the other. Conidia and asci, which 
are used respectively for asexual and sexual reproductions, are usually 
separated from the vegetative hyphae by blocked (non-perforated) septa. 


Asexual reproduction is frequent and involves the production of 
conidiophores that release haploid conidiospores ({link]). Sexual 
reproduction starts with the development of special hyphae from either one 
of two types of mating strains ([link]). The “male” strain produces an 
antheridium and the “female” strain develops an ascogonium. Next, 
cytoplasm of the antheridium and the ascogonium combine in plasmogamy 
without nuclear fusion. Special ascogenous hyphae arise, in which pairs of 
nuclei migrate: one from the “male” strain and one from the “female” 
strain. In each ascus, two or more haploid ascospores fuse their nuclei in 
karyogamy. During sexual reproduction, thousands of asci fill a fruiting 
body called the ascocarp. The diploid nucleus gives rise to haploid nuclei 
by meiosis. These haploid nuclei undergo mitosis and cell divisions to form 
haploid ascospores. The ascospores are then released, germinate, and form 
hyphae that are disseminated in the environment and start new mycelia 


(Link). 


Ascomycete Life Cycle 


cove 


2a 
Spores Mitosis 
Germination Asexual 
eproduction 
Plasmogamy © 


and mitosis: & 

The ascogonium and aes Conidiophore 
antheridium fuse. Mitosis 

and cell division result in 

the formation of many 

dikaryotic hyphae, which Dispersal and 

form a fruiting body zz germination 

called the ascocarp. 

Asci form at the tips 

of these hyphae. 


(@) 


(e)A Ascospores 


Mitosis and 
cell division: 
Eight haploid 
Reproduction ascospores 
are formed. 


SE 


Meiosis: 


An ascus with four 
Ascocarp — haploid nuclei is 
Karyogamy: 4 formed. 


The nuclei in the ro i 
asci fuse to form 
a diploid zygote. 


The lifecycle of an ascomycete is characterized 
by the production of asci during the sexual 
phase. The haploid phase is the predominant 
phase of the life cycle. 


* 
. ee" ome 
>. 


Ascospores 
— ~ — 
, :™*> 


a 


” 


The bright field light 
micrograph shows 
ascospores being released 
from asci in the fungus 
Talaromyces flavus var. 
flavus. (credit: 
modification of work by 
Dr. Lucille Georg, CDC; 
scale-bar data from Matt 
Russell) 


Basidiomycota: The Club Fungi 


The fungi in the Phylum Basidiomycota are easily recognizable under a 
light microscope by their club-shaped fruiting bodies called basidia 
(singular, basidium), which are the swollen terminal cell of a hypha. This 


reproductive organ is the basidiocarp, that contains basidia, and the familiar 
mushroom, commonly seen in fields after rain, on the supermarket shelves, 
or growing on your lawn ([link]). These mushroom-producing 
basidiomyces are sometimes referred to as “gill fungi” because of the 
presence of gill-like structures on the underside of the cap. The “gills” are 
actually compacted hyphae on which the basidia are borne. This group also 
includes shelf fungus, which cling to the bark of trees like small shelves. In 
addition, the basidiomycota includes smuts and rusts, which are important 
plant pathogens; toadstools, and shelf fungi stacked on tree trunks. Most 
edible fungi belong to the Phylum Basidiomycota; however, some 
basidiomycetes produce deadly toxins. For example, Cryptococcus 
neoformans causes severe respiratory illness. 


The fruiting bodies of a 
basidiomycete form a ring ina 
meadow, commonly called 
“fairy ring.” The best-known 
fairy ring fungus has the 
scientific name Marasmius 
oreades. The body of this 
fungus, its mycelium, is 
underground and grows 
outward in a circle. As it grows, 
the mycelium depletes the soil 
of nitrogen, causing the mycelia 


to grow away from the center 
and leading to the “fairy ring” 
of fruiting bodies where there is 
adequate soil nitrogen. (Credit: 
"Cropcircles"/Wikipedia 
Commons)]| 


The lifecycle of basidiomycetes includes alternation of generations ((link]). 
Spores are generally produced through sexual reproduction, rather than 
asexual reproduction. The club-shaped basidium carries spores called 
basidiospores. In the basidium, nuclei of two different mating strains fuse 
(karyogamy), giving rise to a diploid zygote that then undergoes meiosis. 
The haploid nuclei migrate into basidiospores, which germinate and 
generate monokaryotic hyphae. The mycelium that results is called a 
primary mycelium. Mycelia of different mating strains can combine and 
produce a secondary mycelium that contains haploid nuclei of two different 
mating strains. This is the dikaryotic stage of the basidiomyces lifecyle and 
and it is the dominant stage. Eventually, the secondary mycelium generates 
a basidiocarp, which is a fruiting body that protrudes from the ground— 
this is what we think of as a mushroom. The basidiocarp bears the 
developing basidia on the gills under its cap. 


Basidiomycete Life Cycle 


Germination: Basidiospores (n) 


Mycelia form. There are @) © @ 


two mating types (+ and -). 
One) 


Dispersal and 
germination 


Plasmogamy: 

Fusion between Cell division: 
+ and — mating Four 

types results in basidiospores 


formation of a Sexual | ‘are formed 
dikaryotic Reproduction 


mycelium. Basidium with 
four nuclei 
(1n) 


Meiosis: 

Four haploid nuclei 
are formed in the 
basidium. 


Mitosis: 

Under the right ‘O) Zygote 

environmental (2n) 

conditions, a 

basidiocarp forms. Gills 

of the basidiocarp contain 

cells called basidia. Karyogamy: 
aa Basidia form 

Basidia diploid nuclei. 


Basidiocarp 


The lifecycle of a basidiomycete 
alternates generation with a prolonged 
stage in which two nuclei (dikaryon) 
are present in the hyphae. 


Deuteromycota: 


Those fungi that do not display a sexual phase and only reproduce by 
mitospores are classified in the form phylum Deuteromycota. 
Deuteromycota is a polyphyletic group where many species are more 
closely related to organisms in other phyla than to each other; hence it 
cannot be called a true phylum and must, instead, be given the name form 
phylum. Since they do not possess the sexual structures that are used to 
classify other fungi, they are less well described in comparison to other 


divisions. Most members live on land, with a few aquatic exceptions. They 
form visible mycelia with a fuzzy appearance and are commonly known as 
mold. Molecular analysis shows that the closest group to the 
deuteromycetes is the ascomycetes. In fact, some species, such as 
Aspergillus, which were once classified as imperfect fungi, are now 
classified as ascomycetes. 


Reproduction of Deuteromycota is strictly asexual and occurs mostly by 
production of asexual conidiospores ({link]). Some hyphae may recombine 
and form heterokaryotic hyphae. Genetic recombination is known to take 
place between the different nuclei. 


/ y of: y 
S f 
- 
> 
< bf | 
. \ 
‘~. : 
~ | 


a 


/ 
/ eo 


Aspergillus niger is an 
imperfect fungus commonly 
found as a food contaminant. 
The spherical structure in this 

light micrograph is a 
conidiophore. (credit: 
modification of work by Dr. 
Lucille Georg, CDC; scale-bar 
data from Matt Russell) 


The Deuteromycetes have a large impact on everyday human life. The food 
industry relies on them for ripening some cheeses. The blue veins in 
Roquefort cheese and the white crust on Camembert are the result of fungal 
growth. The antibiotic penicillin was originally discovered on an overgrown 
Petri plate, on which a colony of Penicillium fungi killed the bacterial 
growth surrounding it. Many imperfect fungi cause serious diseases, either 
directly as parasites (which infect both plants and humans), or as producers 
of potent toxic compounds, as seen in the aflatoxins released by fungi of the 
genus Aspergillus. 


Glomeromycota: The mitosporic fungi 


The Glomeromycota is a newly established phylum which comprises about 
230 species that all live in close association with the roots of trees. Fossil 
records indicate that trees and their root symbionts share a long 
evolutionary history. It appears that all members of this family form 
arbuscular mycorrhizae: the hyphae interact with the root cells forming a 
mutually beneficial association where the plants supply the carbon source 
and energy in the form of carbohydrates to the fungus, and the fungus 
supplies essential minerals from the soil to the plant. 


The glomeromycetes do not reproduce sexually and do not survive without 
the presence of plant roots. Although they have coenocytic hyphae like the 
zygomycetes, they do not form zygospores. DNA analysis shows that all 
glomeromycetes probably descended from a common ancestor, making 
them a monophyletic lineage. 


Pathogenic Fungi 
Many fungi have negative impacts on other species, including humans and 


the organisms they depend on for food. Fungi may be parasites, pathogens, 
and, in a very few cases, predators. 


Plant Parasites and Pathogens 


The production of enough good-quality crops is essential to our existence. 
Plant diseases have ruined crops, bringing widespread famine. Most plant 
pathogens are fungi that cause tissue decay and eventual death of the host 
({link]). In addition to destroying plant tissue directly, some plant pathogens 
spoil crops by producing potent toxins. Fungi are also responsible for food 
spoilage and the rotting of stored crops. For example, the fungus Claviceps 
purpurea causes ergot, a disease of cereal crops (especially of rye). 
Although the fungus reduces the yield of cereals, the effects of the ergot’s 
alkaloid toxins on humans and animals are of much greater significance: In 
animals, the disease is referred to as ergotism. The most common signs and 
symptoms are convulsions, hallucination, gangrene, and loss of milk in 
cattle. The active ingredient of ergot is lysergic acid, which is a precursor of 
the drug LSD. Smuts, rusts, and powdery or downy mildew are other 
examples of common fungal pathogens that affect crops. 


Some fungal pathogens include (a) green mold on 
grapefruit, (b) fungus on grapes, (c) powdery mildew 
on a zinnia, and (d) stem rust on a sheaf of barley. 
Notice the brownish color of the fungus in (b) Botrytis 
cinerea, also referred to as the “noble rot,” which 
grows on grapes and other fruit. Controlled infection 
of grapes by Botrytis is used to produce strong and 
much-prized dessert wines. (credit a: modification of 


work by Scott Bauer, USDA ARS; credit b: 
modification of work by Stephen Ausmus, USDA 
ARS; credit c: modification of work by David 
Marshall, USDA ARS; credit d: modification of work 
by Joseph Smilanick, USDA ARS) 


Aflatoxins are toxic and carcinogenic compounds released by fungi of the 
genus Aspergillus. Periodically, harvests of nuts and grains are tainted by 
aflatoxins, leading to massive recall of produce, sometimes ruining 
producers, and causing food shortages in developing countries. 


Animal and Human Parasites and Pathogens 


Fungi can affect animals, including humans, in several ways. Fungi attack 
animals directly by colonizing and destroying tissues. Humans and other 
animals can be poisoned by eating toxic mushrooms or foods contaminated 
by fungi. In addition, individuals who display hypersensitivity to molds and 
spores develop strong and dangerous allergic reactions. Fungal infections 
are generally very difficult to treat because, unlike bacteria, fungi are 
eukaryotes. Antibiotics only target prokaryotic cells, whereas compounds 
that kill fungi also adversely affect the eukaryotic animal host. 


Many fungal infections (mycoses) are superficial and termed cutaneous 
(meaning “skin”) mycoses. They are usually visible on the skin of the 
animal. Fungi that cause the superficial mycoses of the epidermis, hair, and 
nails rarely spread to the underlying tissue ({link]). These fungi are often 
misnamed “dermatophytes” from the Greek dermis skin and phyte plant, but 
they are not plants. Dermatophytes are also called “ringworms” because of 
the red ring that they cause on skin (although the ring is caused by fungi, 
not a worm). These fungi secrete extracellular enzymes that break down 
keratin (a protein found in hair, skin, and nails), causing a number of 
conditions such as athlete’s foot, jock itch, and other cutaneous fungal 
infections. These conditions are usually treated with over-the-counter 
topical creams and powders, and are easily cleared. More persistent, 
superficial mycoses may require prescription oral medications. 


“sporangia Sara 2 (A, NNSLN 

ae ee a AN! 
So <5, 4 PE 
Pome <2 fo + Hyphae’* = ) Saha. > 
(b) (c) 


(a) Ringworm presents as a red ring on the skin. (b) 
Trichophyton violaceum is a fungus that causes 
superficial mycoses on the scalp. (c) Histoplasma 
capsulatum, seen in this X-ray as speckling of light 
areas in the lung, is a species of Ascomycota that 
infects airways and causes symptoms similar to the 
flu. (credit a, b: modification of work by Dr. Lucille K. 
Georg, CDC; credit c: modification of work by M 
Renz, CDC; scale-bar data from Matt Russell) 


Systemic mycoses spread to internal organs, most commonly entering the 
body through the respiratory system. For example, coccidioidomycosis 
(valley fever) is commonly found in the southwestern United States, where 
the fungus resides in the dust. Once inhaled, the spores develop in the lungs 
and cause signs and symptoms similar to those of tuberculosis. 
Histoplasmosis ({link]c) is caused by the dimorphic fungus Histoplasma 
capsulatum; it causes pulmonary infections and, in rare cases, swelling of 
the membranes of the brain and spinal cord. Treatment of many fungal 
diseases requires the use of antifungal medications that have serious side 
effects. 


Opportunistic mycoses are fungal infections that are either common in all 
environments or part of the normal biota. They affect mainly individuals 
who have a compromised immune system. Patients in the late stages of 
AIDS suffer from opportunistic mycoses, such as Pneumocystis, which can 
be life threatening. The yeast Candida spp., which is a common member of 
the natural biota, can grow unchecked if the pH, the immune defenses, or 
the normal population of bacteria is altered, causing yeast infections of the 
vagina or mouth (oral thrush). 


Fungi may even take on a predatory lifestyle. In soil environments that are 
poor in nitrogen, some fungi resort to predation of nematodes (small 
roundworms). Species of Arthrobotrys fungi have a number of mechanisms 
to trap nematodes. For example, they have constricting rings within their 
network of hyphae. The rings swell when the nematode touches it and 
closes around the body of the nematode, thus trapping it. The fungus 
extends specialized hyphae that can penetrate the body of the worm and 
slowly digest the hapless prey. 


Beneficial Fungi 


Fungi play a crucial role in the balance of ecosystems. They colonize most 
habitats on Earth, preferring dark, moist conditions. They can thrive in 
seemingly hostile environments, such as the tundra, thanks to a most 
successful symbiosis with photosynthetic organisms, like lichens. Fungi are 
not obvious in the way that large animals or tall trees are. Yet, like bacteria, 
they are major decomposers of nature. With their versatile metabolism, 
fungi break down organic matter that is insoluble and would not be recycled 
otherwise. 


Importance to Ecosystems 


Food webs would be incomplete without organisms that decompose organic 
matter and fungi are key participants in this process. Decomposition allows 
for cycling of nutrients such as carbon, nitrogen, and phosphorus back into 
the environment so they are available to living things, rather than being 


trapped in dead organisms. Fungi are particularly important because they 

have evolved enzymes to break down cellulose and lignin, components of 
plant cell walls that few other organisms are able to digest, releasing their 
carbon content. 


Fungi are also involved in ecologically important coevolved symbioses, 
both mutually beneficial and pathogenic with organisms from the other 
kingdoms. Mycorrhiza, a term combining the Greek roots myco meaning 
fungus and rhizo meaning root, refers to the association between vascular 
plant roots and their symbiotic fungi. Somewhere between 80—90 percent of 
all plant species have mycorrhizal partners. In a mycorrhizal association, 
the fungal mycelia use their extensive network of hyphae and large surface 
area in contact with the soil to channel water and minerals from the soil into 
the plant. In exchange, the plant supplies the products of photosynthesis to 
fuel the metabolism of the fungus. Ectomycorrhizae (“outside” mycorrhiza) 
depend on fungi enveloping the roots in a sheath (called a mantle) and a net 
of hyphae that extends into the roots between cells. In a second type, the 
Glomeromycota fungi form arbuscular mycorrhiza. In these mycorrhiza, the 
fungi form arbuscles, a specialized highly branched hypha, which penetrate 
root cells and are the sites of the metabolic exchanges between the fungus 
and the host plant. Orchids rely on a third type of mycorrhiza. Orchids form 
small seeds without much storage to sustain germination and growth. Their 
seeds will not germinate without a mycorrhizal partner (usually 
Basidiomycota). After nutrients in the seed are depleted, fungal symbionts 
support the growth of the orchid by providing necessary carbohydrates and 
minerals. Some orchids continue to be mycorrhizal throughout their 
lifecycle. 


Lichens blanket many rocks and tree bark, displaying a range of colors and 
textures. Lichens are important pioneer organisms that colonize rock 
surfaces in otherwise lifeless environments such as are created by glacial 
recession. The lichen is able to leach nutrients from the rocks and break 
them down in the first step to creating soil. Lichens are also present in 
mature habitats on rock surfaces or the trunks of trees. They are an 
important food source for caribou. Lichens are not a single organism, but 
rather a fungus (usually an Ascomycota or Basidiomycota species) living in 
close contact with a photosynthetic organism (an alga or cyanobacterium). 


The body of a lichen, referred to as a thallus, is formed of hyphae wrapped 
around the green partner. The photosynthetic organism provides carbon and 
energy in the form of carbohydrates and receives protection from the 
elements by the thallus of the fungal partner. Some cyanobacteria fix 
nitrogen from the atmosphere, contributing nitrogenous compounds to the 
association. In return, the fungus supplies minerals and protection from 
dryness and excessive light by encasing the algae in its mycelium. The 
fungus also attaches the symbiotic organism to the substrate. 


Fungi have evolved mutualistic associations with numerous arthropods. The 
association between species of Basidiomycota and scale insects is one 
example. The fungal mycelium covers and protects the insect colonies. The 
scale insects foster a flow of nutrients from the parasitized plant to the 
fungus. In a second example, leaf-cutting ants of Central and South 
America literally farm fungi. They cut disks of leaves from plants and pile 
them up in gardens. Fungi are cultivated in these gardens, digesting the 
cellulose that the ants cannot break down. Once smaller sugar molecules are 
produced and consumed by the fungi, they in turn become a meal for the 
ants. The insects also patrol their garden, preying on competing fungi. Both 
ants and fungi benefit from the association. The fungus receives a steady 
supply of leaves and freedom from competition, while the ants feed on the 
fungi they cultivate. 


Importance to Humans 


Although we often think of fungi as organisms that cause diseases and rot 
food, fungi are important to human life on many levels. As we have seen, 
they influence the well-being of human populations on a large scale because 
they help nutrients cycle in ecosystems. They have other ecosystem roles as 
well. For example, as animal pathogens, fungi help to control the 
population of damaging pests. These fungi are very specific to the insects 
they attack and do not infect other animals or plants. The potential to use 
fungi as microbial insecticides is being investigated, with several species 
already on the market. For example, the fungus Beauveria bassiana is a 
pesticide that is currently being tested as a possible biological control for 


the recent spread of emerald ash borer. It has been released in Michigan, 
Illinois, Indiana, Ohio, West Virginia, and Maryland. 


The mycorrhizal relationship between fungi and plant roots is essential for 
the productivity of farmland. Without the fungal partner in the root systems, 
80-90% of trees and grasses would not survive. Mycorrhizal fungal 
inoculants are available as soil amendments from gardening supply stores 
and promoted by supporters of organic agriculture. 


We also eat some types of fungi. Mushrooms figure prominently in the 
human diet. Morels, shiitake mushrooms, chanterelles, and truffles are 
considered delicacies ({link]). The humble meadow mushroom, Agaricus 
campestris, appears in many dishes. Molds of the genus Penicillium ripen 
many cheeses. They originate in the natural environment such as the caves 
of Roquefort, France, where wheels of sheep milk cheese are stacked to 
capture the molds responsible for the blue veins and pungent taste of the 
cheese. 


The morel mushroom is 
an ascomycete that is 
much appreciated for its 


delicate taste. (credit: 
Jason Hollinger) 


Fermentation—of grains to produce beer, and of fruits to produce wine—is 
an ancient art that humans in most cultures have practiced for millennia. 
Wild yeasts are acquired from the environment and used to ferment sugars 
into CO, and ethyl alcohol under anaerobic conditions. It is now possible to 
purchase isolated strains of wild yeasts from different wine-making regions. 
Pasteur was instrumental in developing a reliable strain of brewer’s yeast, 
Saccharomyces cerevisiae, for the French brewing industry in the late 
1850s. It was one of the first examples of biotechnology patenting. Yeast is 
also used to make breads that rise. The carbon dioxide they produce is 
responsible for the bubbles produced in the dough that become the air 
pockets of the baked bread. 


Many secondary metabolites of fungi are of great commercial importance. 
Antibiotics are naturally produced by fungi to kill or inhibit the growth of 
bacteria, and limit competition in the natural environment. Valuable drugs 
isolated from fungi include the immunosuppressant drug cyclosporine 
(which reduces the risk of rejection after organ transplant), the precursors of 
steroid hormones, and ergot alkaloids used to stop bleeding. In addition, as 
easily cultured eukaryotic organisms, some fungi are important model 
research organisms including the red bread mold Neurospora crassa and the 
yeast, S. cerevisiae. 


Lichens, Protists and Green Algae 


Introduction 

" A process which led from the amoeba to man appeared to the philosophers to be obviously a progress— 
though whether the amoeba would agree with this opinion is not known." Bertrand Russell, from "Current 
Tendencies", delivered as the first of a series of Lowell Lectures in Boston (Mar 1914). 


Lichens 


Lichens display a range of colors and textures ({link]) and can survive in the most unusual and hostile 
habitats. They cover rocks, gravestones, tree bark, and the ground in the tundra where plant roots cannot 
penetrate. Lichens can survive extended periods of drought, when they become completely desiccated, 
and then rapidly become active once water is available again. 


Lichens have many forms. They may be (a) crust-like, (b) hair-like, or (c) leaf-like. (credit a: 
modification of work by Jo Naylor; credit b: modification of work by "djpmapleferryman"/Flickr; 
credit c: modification of work by Cory Zanker) 


Lichens are an example of a mutualism, in which a fungus (usually a member of the Ascomycota or 
Basidiomycota phyla) lives in close contact with a photosynthetic organism (a eukaryotic alga or a 
prokaryotic cyanobacterium) ([link]). Generally, neither the fungus nor the photosynthetic organism can 
survive alone outside of the symbiotic relationship. The body of a lichen, referred to as a thallus, is 
formed of hyphae wrapped around the photosynthetic partner. The photosynthetic organism provides 
carbon and energy in the form of carbohydrates. Some cyanobacteria fix nitrogen from the atmosphere, 
contributing nitrogenous compounds to the association. In return, the fungus supplies minerals and 
protection from dryness and excessive light by encasing the algae in its mycelium. The fungus also 
attaches the symbiotic organism to the substrate. 


o 


This cross-section of a lichen 
thallus shows the (a) upper 
cortex of fungal hyphae, which 
provides protection; the (b) 
algal zone where photosynthesis 
occurs, the (c) medulla of 
fungal hyphae, and the (d) 
lower cortex, which also 
provides protection and may 
have (e) rhizines to anchor the 
thallus to the substrate. 


Lichens grow very slowly, expanding a few millimeters per year. Both the fungus and the alga participate 
in the formation of dispersal units for reproduction. Lichens produce soredia, clusters of algal cells 
surrounded by mycelia. Soredia are dispersed by wind and water and form new lichens. 


Lichens are extremely sensitive to air pollution, especially to abnormal levels of nitrogen and sulfur. The 
U.S. Forest Service and National Park Service can monitor air quality by measuring the relative 
abundance and health of the lichen population in an area. Lichens fulfill many ecological roles. Lichens 
are often early colonizers of bare rock. Caribou and reindeer eat lichens, and they provide cover for small 
invertebrates that hide in the mycelium. In the production of textiles, weavers used lichens to dye wool 
for many centuries until the advent of synthetic dyes. 


Protists 


Amoebae are just one of the creatures that are lumped into the Kingdom Protista, and amoebae and 
philosophers do share a common ancestor, as Russell points out. In the span of the last several decades, 
the Kingdom Protista has been disassembled and rearranged, as DNA sequence analyses have revealed 
new genetic (and therefore evolutionary) relationships among these eukaryotes. Moreover, protists species 
that exhibit similar morphological features may not be closely related, but may have evolved analogous 
structures because of similar selective pressures — rather than because of recent common ancestry. This 
phenomenon, called convergent evolution, is one reason why protist classification is so challenging. The 


emerging classification scheme groups the entire domain Eukarya into six “supergroups” that contain all 
of the protists as well as animals, plants, and fungi that evolved from a common ancestor ([link]). The 
supergroups are hypothesized to be monophyletic, meaning that all organisms within each supergroup are 
hypothesized to have evolved from a single common ancestor, and thus all members are more closely 
related to each other than to organisms outside that group. There is still evidence lacking for the 
monophyly of some groups. 


Alveolates 


Stramenopiles 


Common 
eukaryotic 
ancestor 
Red algae 


Chlorophytes 
(green algae) 


Charophytes 
(green algae) 


Land plants 


Slime molds 
Gymnamoebas 
Entamoebas 


This diagram shows a proposed classification of the 
domain Eukara. Currently, the domain Eukarya is 
divided into six supergroups. Within each supergroup 
are multiple kingdoms. Dotted lines indicate 
suggested evolutionary relationships that remain 
under debate. 


The classification of eukaryotes is still in flux, and the six supergroups may be modified or replaced by a 
more appropriate hierarchy as genetic, morphological, and ecological data accumulate. Keep in mind that 
the classification scheme presented here is just one of several hypotheses, and the true evolutionary 


relationships are still to be determined. For this module, we are focusing on the Archaeplastida which 
contain the green algae - the group of organisms most closely related to plants. 


Archaeplastida (Red Algae, Green Algae and Plants) 


Red algae and green algae are included in the supergroup Archaeplastida. It was from a common ancestor 
of these organisms that the land plants evolved, since their closest relatives are found in this group. 
Molecular evidence supports that all Archaeplastida are descendents of an endosymbiotic relationship 
between a heterotrophic protist and a cyanobacterium. The red and green algae include unicellular, 
multicellular, and colonial forms. 


Red Algae 


Red algae, or rhodophytes, lack flagella and range in size from microscopic unicellular forms to large, 
multicellular forms grouped into the informal 'seaweed' category. Most red algae are multicellular. The 
red algae life cycle is an alternation of generations (explained in next section). Some species of red algae 
contain phycoerythrins, photosynthetic accessory pigments that are red in color and outcompete the green 
tint of chlorophyll, making these species appear as varying shades of red. Other species classified as red 
algae lack phycoerythrins and are parasites. Red algae are common in tropical waters where they have 
been detected at depths of 260 meters. Other red algae exist in terrestrial or freshwater environments. 


Red Algae are an economically important food source and additive. Have you ever eaten sushi rolls? If 
so, the crispy sheets wrapped around the rice are from the genus Porphyra (Japanese "nori"). The food 
stabilizer carrageenan is found in ice cream, yogurt and other food stuffs and is an extract from red algae. 
Another extract from red algae commonly used as a thickener and as vegetarian substitute for gelatin is 
agar. Agar is also commonly used by microbiologists as a solid substrate to contain culture media in order 
to grow bacteria. 


Green Algae: Chlorophytes and Charophytes 


The most abundant group of algae are the green algae. The green algae exhibit similar features to the land 
plants. The cell walls of green algae and land plants are made of cellulose and the chloroplasts of both 
groups contain chlorophylls a and b. The hypothesis that this group of protists shared a relatively recent 
common ancestor with land plants is well supported. The green algae are subdivided into the chlorophytes 
and charophytes. The charophytes are the closest living relatives to land plants and resemble them in 
morphology and reproductive strategies. Charophytes are common in wet habitats, and their presence 
often signals a healthy ecosystem. 


Green algae are as a group of organisms an integral part of a functional ecosystem, and humans have been 
using green algae as a food source and as a medicine for a long time. In aquatic environments, green algae 
are a Major primary producer and release a substantial amount of oxygen in the system. So a healthy 
ecosystem is dependent on a healthy population of green algae. As a economic benefit to humans, green 
algae are used a food source (Asakusa Nori) for humans and are used a food thickening agent. Green 
algae are used in the agricultural industry as a food source for cattle, and as fertilizer. 


The chlorophytes exhibit great diversity of form and function. Chlorophytes primarily inhabit freshwater 
and damp soil, and are a common component of plankton. Chlamydomonas is a simple, unicellular 
chlorophyte with a pear-shaped morphology and two opposing, anterior flagella that guide this protist 
toward light sensed by its eyespot. 


Volvox is an example of multicellularity in the Chlorophytes ({link]). Volvox colonies contain 500 to 
60,000 cells, each with two flagella, contained within a hollow, spherical matrix composed of a gelatinous 
glycoprotein secretion. Volvox moves by rolling in a coordinated fashion. The cells forming the sphere on 
the outside do not reproduce while the green cells inside do reproduce, demonstrating division of labor. 


Volvox aureus is a green alga in the supergroup Archaeplastida. 

This species exists as a colony, consisting of cells immersed in 

a gel-like matrix and intertwined with each other via hair-like 
cytoplasmic extensions. (credit: Dr. Ralf Wagner) 


True multicellular organisms, such as the sea lettuce, Ulva, are represented among the chlorophytes. In 
addition, some chlorophytes exist as large, multinucleate, single cells. Species in the genus Caulerpa 
exhibit flattened fern-like foliage and can reach lengths of 3 meters ([link]). Caulerpa species undergo 
nuclear division, but their cells do not complete cytokinesis, remaining instead as massive and elaborate 
single cells. 


Caulerpa taxifolia is a chlorophyte 
consisting of a single cell 
containing potentially thousands 
of nuclei. (credit: NOAA) 


Charophytes are the closest related green algae to land plants, this conclusion was drawn from studies of 
nuclear and chloroplast genes from many different types of plants and algae. In addition to the similarities 
listed above, there a some additional structural similarities such as cellulose-synthesizing proteins, the 
structure of the flagellated sperm and the gamete producing structures that suggest that land plants arose 


from within the charophyta group. This does not mean land plants are descended from living green algae, 
but it does allow us to explore the algal ancestor to land plants. For example, the exploration of the Chara 
life cycle [link] allows us visualize the similarities between the life cycle of green algae and land plants. 


Chara Life Cycle 


Haploid (N) 
Mitosi, 

0 
£ 
aS 

. \\ o. 
| e ®, 
Male \ Female 
Spore Beamer. Gametes 
of 


Diploid (2N) = 


Simplified life cycle of Chara. (Work by Robbie Bear, Images credited to "Chara antheridia L" by Jon 
Houseman - Jon Houseman and Matthew Ford. Licensed under CC BY-SA 4.0 via Wikimedia 
Commons - 
http://commons. wikimedia.org/wiki/File:Chara_antheridia_L.jpg#/media/File:Chara_antheridia_L.jp 
g "Chara oogonium" by Jon Houseman - Jon Houseman and Matthew Ford. Licensed under CC BY- 
SA 4.0 via Wikimedia Commons - 
http://commons. wikimedia.org/wiki/File:Chara_oogonium.jpg#/media/File:Chara_oogonium.jpg 
"Chara braunii 1" by Show_ryu - Own work. Licensed under CC BY-SA 3.0 via Wikimedia 
Commons - 
http://commons. wikimedia.org/wiki/File: Chara_braunii_1.JPG#/media/File:Chara_braunii_1.JPG) 


Early Plant Life 


Introduction 

"T observed on most collected stones the imprints of innumerable plant 
fragments which were so different from those which are growing in the 
Lyonnais, in the nearby provinces, and even in the rest of France, that I felt 
like collecting plants in a new world... The number of these leaves, the way 
they separated easily, and the great variety of plants whose imprints I saw, 
appeared to me just as many volumes of botany representing in the same 
quarry the oldest library of the world. " Antoine de Jussieu, French 
physician and botanist, 1718 


The kingdom Plantae constitutes a large and varied group of organisms, 
which have been on the planet for a very long time. There are more than 
300,000 species of catalogued plants, including the fossil plants that de 
Jussieu references in the epigraph above. Of these, more than 260,000 are 
seed plants. Mosses, ferns, conifers, and flowering plants are all members 
of the plant kingdom. While there is some disagreement about the 
relationships between Chlorophytes, Charophytes, and Plantae, there are 
several unique characteristics which these groups share. Only green algae 
and plants use chlorophyll a and b plus carotene in a particular ratio. They 
share the trait of cellulose-rich cell walls, and there is strong molecular 
support for their close relationship. 


The ancestors of the green algae became photosynthetic by engulfing a 
green, photosynthetic bacterium about 1.65 billion years ago. This captured 
bacterium evolved into a chloroplast. That algal line evolved into the 
Charophytes, bryophytes, seedless vascular plants, gymnosperms, and 
angiosperms. 


Several other groups of eukaryotes have common names that include 
‘algae.’ In the latest classification red algae are included in Archaeplastida, 
while brown algae and golden algae are in a separate supergroup. In 
contrast to the green algae, red, golden, and brown algae all became 
photosynthetic by secondary, or even tertiary, endosymbiotic events. In 
other words, the cells that evolved into red, brown, or golden algae all 
engulfed cells that had already engulfed a photosynthetic bacterium. These 


algae are also photosynthetic autotrophs, but they did not diversify to the 
same extent as the Charophytes, nor did they colonize land. 


Plant Adaptations to Life on Land 


In order for plants to invade land, they had to contend with several 
challenges in the terrestrial environment. Water has been described as “the 
stuff of life.” The cell’s interior is a watery soup: in this medium, most 
small molecules can dissolve and diffuse rapidly, and the majority of the 
chemical reactions of metabolism take place. The first challenge, 
Desiccation, or drying out, is a constant danger for an organism exposed to 
air. Even when parts of a plant are close to a source of water, the aerial 
structures are likely to dry out. Second, Water also provides buoyancy to 
organisms. On land, plants need to develop structural support in a medium 
that does not give the same support as water. The organism is also subject to 
bombardment by mutagenic radiation, because air does not filter out 
ultraviolet rays of sunlight like water does. Additionally, the male gametes 
must reach the female gametes using new strategies, because swimming is 
no longer possible. Lastly, both gametes and zygotes must be protected 
from desiccation. The successful land plants developed strategies to deal 
with all of these challenges. Not all adaptations appeared at once. Some 
species never moved very far from the aquatic environment, whereas others 
went on to conquer the driest environments on Earth. 


To balance these survival challenges, life on land offers several advantages. 
First, sunlight is abundant. Water acts as a filter, altering the spectral quality 
of light absorbed by the photosynthetic pigment chlorophyll. Second, 
carbon dioxide is more readily available in air than in water, since it 
diffuses faster in air. Third, land plants evolved before land animals; 
therefore, until dry land was colonized by animals, no predators threatened 
plant life. This situation changed as animals emerged from the water and 
fed on the abundant sources of nutrients in the established flora. In turn, 
plants developed strategies to deter predation: from spines and thorns to 
toxic chemicals. 


Early land plants, like the early land animals, did not live very far from an 
abundant source of water and developed survival strategies to combat 


dryness. One of these strategies is called tolerance. Many mosses, for 
example, can dry out to a brown and brittle mat, but as soon as rain or a 
flood makes water available, mosses will absorb it and are restored to their 
healthy green appearance. Another strategy is to colonize environments 
with high humidity, where droughts are uncommon. Ferns, which are 
considered an early lineage of plants, thrive in damp and cool places such 
as the understory of temperate forests. Later, plants moved away from moist 
or aquatic environments using resistance to desiccation, rather than 
tolerance. These plants, like cacti, minimize the loss of water to such an 
extent they can survive in extremely dry environments. 


The most successful adaptation was the development of new structures that 
gave plants the advantage when colonizing new and dry environments. Four 
major adaptations are found in all terrestrial plants: the alternation of 
generations, a sporangium in which the spores are formed, a gametangium 
that produces haploid cells, and apical meristem tissue in roots and shoots. 
The evolution of a waxy cuticle and a cell wall with lignin also contributed 
to the success of land plants. These adaptations are noticeably lacking in the 
closely related green algae. 


Alternation of Generations 


Alternation of generations describes a life cycle in which an organism has 
both haploid and diploid multicellular stages ([link]). 


Generalized Plant Life Cycle 


Alternation of generations between the 1N gametophyte and 2N 
sporophyte is shown. Work by Eva Horne and Robert A. Bear 


Most plants exhibit alternation of generations, wherein the haploid 
multicellular form, known as a gametophyte, is followed in the 
development sequence by a multicellular diploid organism: the sporophyte. 
The gametophyte gives rise to the gametes (reproductive cells) by mitosis. 
This can be the most obvious phase of the life cycle of the plant, as in the 
mosses, or it can occur in a microscopic structure, such as a pollen grain, in 
the higher plants (a common collective term for the vascular plants). The 
sporophyte stage is barely noticeable in lower plants (the collective term for 
the plant groups of mosses, liverworts, and hornworts). Towering trees are 
the diploid, sporophyte phase in the lifecycles of plants such as sequoias 
and pines. 


Protection of the embryo is a major requirement for land plants. Embryos 
have a high surface area to volume ratio, and thus are vulnerable to 
desiccation and other environmental hazards. In both seedless and seed 
plants, the female gametophyte provides protection and nutrients to the 
embryo as it develops into the new generation of sporophyte. This 
distinguishing feature of land plants gave the group its alternate name of 
embryophytes. 


Sporangia in Seedless Plants 


The sporophyte of seedless plants is diploid and results from syngamy 
(fusion) of two gametes. The sporophyte bears the sporangia (singular, 
sporangium): organs that first appeared in the land plants. The term 
“sporangia” literally means “spore in a vessel,” as it is a reproductive sac 
that contains spores [link]. Inside the multicellular sporangia, the diploid 
sporocytes, or mother cells, produce haploid spores by meiosis, where the 
2N chromosome number is reduced to 1N (note that many plant 
sporophytes are polyploid: for example, durum wheat is tetraploid (4N), 
bread wheat is hexaploid (6N), and some ferns are 1000-ploid). The spores 
are later released by the sporangia and disperse in the environment. Two 
different types of spores are produced in land plants, resulting in the 
separation of sexes at different points in the lifecycle. Seedless non- 
vascular plants produce only one kind of spore and are called 
homosporous. The gametophyte phase is dominant in these plants. After 
germinating from a spore, the resulting gametophyte produces both male 
and female gametangia, usually on the same individual. In contrast, 
heterosporous plants produce two morphologically different types of 
spores. The male spores are called microspores, because of their smaller 
size, and develop into the male gametophyte; the comparatively larger 
megaspores develop into the female gametophyte. Heterospory is observed 
in a few seedless vascular plants and in all seed plants. 


Spore-producing sacs called 
sporangia grow at the ends of 
long, thin stalks in this photo of 
the moss Esporangios bryum. 
(credit: Javier Martin) 


When the haploid spore germinates in a hospitable environment, it grows 
into a multicellular gametophyte by mitosis. The gametophyte supports the 
zygote formed from the fusion of gametes and the resulting young 
sporophyte (vegetative form). The cycle then begins anew. 


The spores of seedless plants are surrounded by thick cell walls containing 
a tough polymer known as sporopollenin. This complex substance is 
characterized by long chains of organic molecules related to fatty acids and 
carotenoids: hence the yellow color of most pollen. Sporopollenin is 
unusually resistant to chemical and biological degradation. In seed plants, 
which use pollen (the microspore) to transfer the male sperm to the female 
egg, the toughness of sporopollenin explains the existence of well- 
preserved pollen fossils. Sporopollenin was once thought to be an 
innovation of land plants; however, the green algae Coleochaetes forms 
spores that contain sporopollenin. 


Gametangia in Seedless Plants 


Gametangia (singular, gametangium) are structures observed on 
multicellular haploid gametophytes. In the gametangia, precursor cells give 
rise to gametes by mitosis. The male gametangium (antheridium) releases 
sperm. Many seedless plants produce sperm equipped with flagella that 
enable them to swim in a moist environment to the archegonia: the female 
gametangium. The embryo develops inside an archegonium into a 
multicellular sporophyte. Gametangia are prominent in seedless plants, but 
are very rarely found in seed plants. 


Apical Meristems 


Shoots and roots of plants increase in length through rapid cell division in a 
tissue called the apical meristem, which is a small zone of cells found at the 
shoot tip or root tip ([link]). The apical meristem is made of 
undifferentiated cells that continue to proliferate throughout the life of the 
plant. Meristematic cells give rise to all the specialized tissues of the 
organism. Elongation of the shoots and roots allows a plant to access 
additional space and resources: light in the case of the shoot, and water and 
minerals in the case of roots. A separate meristem, called the lateral 
meristem, produces cells that increase the diameter of tree trunks. 


Apical meristem 


Root cap 


Addition of new cells in a 
root occurs at the apical 


meristem. Subsequent 
enlargement of these cells 
causes the organ to grow and 
elongate. The root cap 
protects the fragile apical 
meristem as the root tip is 
pushed through the soil by 
cell elongation. 


Additional Land Plant Adaptations 


As plants adapted to dry land and became independent from the constant 
presence of water in damp habitats, new organs and structures made their 
appearance. Early land plants did not grow more than a few inches off the 
ground, competing for light on these low mats. By developing a shoot and 
growing taller, individual plants captured more light. Because air offers 
substantially less support than water, land plants incorporated more rigid 
molecules in their stems (and later, tree trunks). In small organisms such as 
single-celled algae, simple diffusion suffices to distribute water and 
nutrients throughout the organism. However, for plants to evolve larger 
forms, the evolution of vascular tissue for the distribution of water and 
solutes was a prerequisite. The vascular system contains xylem and phloem 
tissues. Xylem conducts water and minerals absorbed from the soil up to 
the shoot, while phloem transports food derived from photosynthesis 
throughout the entire plant. A root system evolved to take up water and 
minerals from the soil, and to anchor the increasingly taller shoot in the soil. 


In land plants, a waxy, waterproof cover called a cuticle protects the leaves 
and stems from desiccation. However, the cuticle also prevents intake of 
carbon dioxide needed for the synthesis of carbohydrates through 
photosynthesis. To overcome this, stomata or pores that open and close to 
regulate traffic of gases and water vapor evolved in plants as they moved 
away from moist environments into drier habitats. 


Lignin is a complex polymer predominantly found in the cell walls of 
xylem, it forms crosslinks between the cellulose molecules. Since lignin is 
interwoven into the cell walls, it adds strength to the cell wall and therefore 
the entire plant. In addition, lignin is a hydrophobic compound that allows 
for the more efficient transport of water in the vascular tissue. 


Water filters ultraviolet-B (UVB) light, which is harmful to all organisms, 
especially those that must absorb light to survive. This filtering does not 
occur for land plants. This presented an additional challenge to land 
colonization, which was met by the evolution of biosynthetic pathways for 
the synthesis of protective flavonoids and other compounds: pigments that 
absorb UV wavelengths of light and protect the aerial parts of plants from 
photodynamic damage. 


Plants cannot avoid being eaten by animals. Instead, they synthesize a large 
range of poisonous secondary metabolites: complex organic molecules such 
as alkaloids, whose noxious smells and unpleasant taste deter animals. 
These toxic compounds can also cause severe diseases and even death, thus 
discouraging predation. Humans have used many of these compounds for 
centuries as drugs, medications, or spices. In contrast, as plants co-evolved 
with animals, the development of sweet and nutritious metabolites lured 
animals into providing valuable assistance in dispersing pollen grains, fruit, 
or seeds. Plants have been enlisting animals to be their helpers in this way 
for hundreds of millions of years. 


Evolution of Land Plants 


No discussion of the evolution of plants on land can be undertaken without 
a brief review of the timeline of the geological eras. The early era, known 
as the Paleozoic, is divided into six periods. It starts with the Cambrian 
period, followed by the Ordovician, Silurian, Devonian, Carboniferous, and 
Permian. The major event to mark the Ordovician, more than 500 million 
years ago, was the colonization of land by the ancestors of modern land 
plants. Fossilized cells, cuticles, and spores of early land plants have been 
dated as far back as the Ordovician period in the early Paleozoic era. The 
oldest-known vascular plants have been identified in deposits from the 
Devonian. One of the richest sources of information is the Rhynie chert, a 


sedimentary rock deposit found in Rhynie, Scotland ([link]), where 
embedded fossils of some of the earliest vascular plants have been 
identified. 


(b) 


This Rhynie chert contains fossilized material from 
vascular plants. The area inside figure a contains 
bulbous underground stems called corms, and root- 
like structures called rhizoids. (credit b: modification 
of work by Peter Coxhead based on original image 
by “Smith609”/Wikimedia Commons; scale-bar data 
from Matt Russell) 


Paleobotanists distinguish between extinct species, as fossils, and extant 
species, which are still living. The extinct vascular plants, classified as 
zosterophylls and trimerophytes, most probably lacked true leaves and roots 
and formed low vegetation mats similar in size to modern-day mosses, 
although some trimetophytes could reach one meter in height. The later 
genus Cooksonia, which flourished during the Silurian, has been 


extensively studied from well-preserved examples. Imprints of Cooksonia 
show slender branching stems ending in what appear to be sporangia. From 
the recovered specimens, it is not possible to establish for certain whether 
Cooksonia possessed vascular tissues. Fossils indicate that by the end of the 
Devonian period, ferns, horsetails, and seed plants populated the landscape, 
giving rising to trees and forests. This luxuriant vegetation helped enrich 
the atmosphere in oxygen, making it easier for air-breathing animals to 
colonize dry land. Plants also established early symbiotic relationships with 
fungi, creating mycorrhizae: a relationship in which the fungal network of 
filaments increases the efficiency of the plant root system, and the plants 
provide the fungi with byproducts of photosynthesis. 


Note: 

Career Connection 

Paleobotanist 

How organisms acquired traits that allow them to colonize new 
environments—and how the contemporary ecosystem is shaped—are 
fundamental questions of evolution. Paleobotany (the study of extinct 
plants) addresses these questions through the analysis of fossilized 
specimens retrieved from field studies, reconstituting the morphology of 
organisms that disappeared long ago. Paleobotanists trace the evolution of 
plants by following the modifications in plant morphology: shedding light 
on the connection between existing plants by identifying common 
ancestors that display the same traits. This field seeks to find transitional 
species that bridge gaps in the path to the development of modern 
organisms. Fossils are formed when organisms are trapped in sediments or 
environments where their shapes are preserved. Paleobotanists collect 
fossil specimens in the field and place them in the context of the geological 
sediments and other fossilized organisms surrounding them. The activity 
requires great care to preserve the integrity of the delicate fossils and the 
layers of rock in which they are found. 

One of the most exciting recent developments in paleobotany is the use of 
analytical chemistry and molecular biology to study fossils. Preservation of 
molecular structures requires an environment free of oxygen, since 
oxidation and degradation of material through the activity of 


microorganisms depend on its presence. One example of the use of 
analytical chemistry and molecular biology is the identification of 
oleanane, a compound that deters pests. Up to this point, oleanane 
appeared to be unique to flowering plants; however, it has now been 
recovered from sediments dating from the Permian, much earlier than the 
current dates given for the appearance of the first flowering plants. 
Paleobotanists can also study fossil DNA, which can yield a large amount 
of information, by analyzing and comparing the DNA sequences of extinct 
plants with those of living and related organisms. Through this analysis, 
evolutionary relationships can be built for plant lineages. 

Paleobotanists must be cautious when drawing conclusions from the 
analysis of molecular fossils. Chemical materials of interest degrade 
rapidly when exposed to air during their initial isolation, as well as in 
further manipulations. There is always a risk of contaminating the 
specimens with extraneous material, mostly from microorganisms. 
Nevertheless, as technology is refined, the analysis of DNA from fossilized 
plants will provide invaluable information on the evolution of plants and 
their adaptation to an ever-changing environment. 


The Major Divisions of Land Plants 


Land plants are classified into two major groups according to the absence or 
presence of vascular tissue, as detailed in [link]. Plants that lack vascular 
tissue, which is formed of specialized cells for the transport of water and 
nutrients, are referred to as non-vascular plants. Liverworts, mosses, and 
hornworts are seedless, non-vascular plants that likely appeared early in 
land plant evolution. Vascular plants developed a network of cells that 
conduct water and solutes. The first vascular plants appeared in the middle 
Paleozoic and were probably similar to lycophytes, which include club 
mosses (not to be confused with the mosses) and the pterophytes (ferns, 
horsetails, and whisk ferns). Lycophytes and pterophytes are referred to as 
seedless vascular plants, because they do not produce seeds. The seed 
plants, or spermatophytes, form the largest group of all existing plants, and 
hence dominate the landscape. Seed plants include Gymnosperms, most 
notably conifers (Gymnosperms), which produce “naked seeds,” and the 


most successful of all plants, the flowering plants (Angiosperms). 
Angiosperms protect their seeds inside chambers at the center of a flower; 
the walls of the chamber later develop into a fruit. 


Note: 
Flowers and Fruits 
Angiosperms 
Seeds Gnetophytes 
Conifers 
Vascular Ginkgos Gymnosperms 
Tissue Cycads 
True ferns 
Horsetails Seedless 
Whisk ferns Vascular 
Land Club mosses 
Plants 
Mosses 
Hornworts Bryophytes 
Liverworts 
500 400 300 200 100 0 


Time (millions of year ago) 


This figure shows the major divisions of green plants and when 
various adaptations for land life evolved. Work by Robert A. Bear 


Bryophytes 


Introduction 

"It was to Hofmeister, working as a young man, an amateur and enthusiast, 
in the early morning hours of summer months, before business, at Leipzig 
in the years before 1851, that the vision first appeared of a common type of 
Life-Cycle, running through Mosses and Ferns to Gymnosperms and 
Flowering Plants, linking the whole series in one scheme of reproduction 
and life-history." Arthur Harry Church, 1919. As quoted in E.J.H. Corner, 
The Life of Plants (1964) 


The commonality of the plant life cycle unites the Plant Kingdom, 
indicating that it appeared very early in the evolution of plants. The 
Bryophytes are the group of plants that are the closest extant relative of 
those early terrestrial plants. The first bryophytes (liverworts) most likely 
appeared in the Ordovician period, about 450 million years ago. Because of 
the lack of lignin and other resistant structures, the likelihood of bryophytes 
forming fossils is rather small. Some spores protected by sporopollenin 
have survived and are attributed to early bryophytes. By the Silurian period, 
however, vascular plants had spread through the continents. This 
compelling fact is used as evidence that non-vascular plants must have 
preceded the Silurian period. 


More than 25,000 species of bryophytes thrive in mostly damp habitats, 
although some live in deserts. They constitute the major flora of 
inhospitable environments like the tundra, where their small size and 
tolerance to desiccation offer distinct advantages. They generally lack lignin 
and do not have actual tracheids (xylem cells specialized for water 
conduction). Rather, water and nutrients circulate inside specialized 
conducting cells. Although the term non-tracheophyte is more accurate, 
bryophytes are commonly called non-vascular plants. 


In a bryophyte, all the conspicuous vegetative organs—including the 
photosynthetic leaf-like structures, the thallus, stem, and the rhizoid that 
anchors the plant to its substrate—belong to the haploid organism or 
gametophyte. The sporophyte is barely noticeable. The gametes formed by 
bryophytes swim with a flagellum, as do gametes in a few of the vascular 
plants. The sporangium—the multicellular sexual reproductive structure—is 


present in bryophytes and absent in the majority of algae. The bryophyte 
embryo also remains attached to the parent plant, which protects and 
nourishes it. This is a characteristic of land plants. 


The Bryophyte life cycle follows the pattern of alternation of generations as 
shown in [link]. The most familiar structure is the haploid gametophyte, 
which germinates from a haploid spore. Cells similar to an apical meristem 
actively divide and give rise to the photosynthetic stem and leaf-like 
structures. Sperm and egg producing structures form on separate or the 
same stems. Sperm swim along the bryophte and unite with the egg inside 
the egg-producing structure (archegonium). The zygote, protected by this 
structure, divides and grows into a sporophyte, still attached to the 
gametophyte. The sporophyte forms spores by meiosis; these disperse and 
will form new gametophytes. 


Bryophyte Life Cycle 


This illustration shows the generalized life cycle of bryophytes. Work 
by Eva Horne and Robert A. Bear 


The bryophytes are divided into three phyla: the liverworts or 
Hepaticophyta, the hornworts or Anthocerotophyta, and the mosses or true 
Bryophyta. The organisms in these three phyla share the following 
characteristics. Bryophytes lack vascular tissue, lack true leaves, lack seeds, 
use spores as a means of dispersal and have the gametophyte generation as 
the dominant (conspicuous) part of the life cycle. Even with all these 
characteristics in common, molecular and other evidence suggests that they 
do not form a single clade (a group that includes one common ancestor and 
all of its descendants) 


Liverworts 


Liverworts (Hepaticophyta) are viewed as the plants most closely related 
to the ancestor that moved to land. Liverworts have colonized every 
terrestrial habitat on Earth and diversified to more than 7,000 existing 
species ({link]). Some gametophytes form lobate green structures, as seen in 
[link]. The shape is similar to the lobes of the liver, and hence provides the 
origin of the name given to the phylum. Openings that allow the movement 
of gases may be observed in liverworts. However, these openings are not 
stomata, because they do not actively open and close. The plant takes up 
water over its entire surface and has no cuticle to prevent desiccation. 


This 1904 drawing shows the 
variety of forms of 
liverworts. 


A liverwort, Lunularia cruciata, 
displays its lobate, flat thallus. The 
organism in the photograph is in 
the gametophyte stage. 


The lifecycle of a liverwort starts with the release of haploid spores from 
the sporangium that developed on the sporophyte. Spores disseminated by 
wind or water germinate into flattened thalli attached to the substrate by 
thin, single-celled filaments. Male and female gametangia develop on 
separate, individual plants. Once released, male gametes swim with the aid 
of their flagella to the female gametangium (the archegonium), and 
fertilization ensues. The zygote grows into a small sporophyte still attached 
to the parent gametophyte. It will give rise, by meiosis, to the next 
generation of spores. Liverwort plants can also reproduce asexually, by the 
breaking of branches or the spreading of leaf fragments called gemmae. In 
this latter type of reproduction, the gemmae—small, intact, complete pieces 
of plant that are produced in a cup on the surface of the thallus are splashed 
out of the cup by raindrops. The gemmae then land nearby and develop into 
gametophytes. 


Hornworts 


The hornworts (Anthocerotophyta) have colonized a variety of habitats on 
land, although they are never far from a source of moisture. The short, blue- 
green gametophyte is the dominant phase of the lifecycle of a hornwort. 
The narrow, pipe-like sporophyte is the defining characteristic of the group. 
The sporophytes emerge from the parent gametophyte and continue to grow 
throughout the life of the plant ([link]). 


Hornworts grow a tall and 
slender sporophyte. (credit: 
modification of work by 
Jason Hollinger) 


Stomata appear in the hormworts and are abundant on the sporophyte. 
Photosynthetic cells in the thallus contain a single chloroplast. Meristem 
cells at the base of the plant keep dividing and adding to its height. Many 
hornworts establish symbiotic relationships with cyanobacteria that fix 
nitrogen from the environment. 


The lifecycle of hornworts follows the general pattern of alternation of 
generations. The gametophytes grow as flat thalli on the soil with 
embedded gametangia. Flagellated sperm swim to the archegonia and 
fertilize eggs. The zygote develops into a long and slender sporophyte that 
eventually splits open, releasing spores. The haploid spores germinate and 
give rise to the next generation of gametophyte. 


Mosses 


More than 10,000 species of mosses have been catalogued. Their habitats 
vary from the tundra, where they are the main vegetation, to the understory 
of tropical forests. In the tundra, the mosses’ shallow rhizoids allow them to 
fasten to a substrate without penetrating the frozen soil. Mosses slow down 
erosion, store moisture and soil nutrients, and provide shelter for small 


animals as well as food for larger herbivores, such as the musk ox. Mosses 
are very sensitive to air pollution and are used to monitor air quality. They 
are also sensitive to copper salts, so these salts are a common ingredient of 
compounds marketed to eliminate mosses from lawns. 


Mosses form diminutive gametophytes, which are the dominant phase of 
the lifecycle. Green, flat structures—resembling true leaves, but lacking 
vascular tissue—are attached in a spiral to a central stalk. The plants absorb 
water and nutrients directly through these leaf-like structures. Some mosses 
have small branches. Some primitive traits of green algae, such as 
flagellated sperm, are still present in mosses that are dependent on water for 
reproduction. Other features of mosses are clearly adaptations to dry land. 
For example, stomata are present on the stems of the sporophyte, and a 
primitive vascular system runs up the sporophyte’s stalk. Additionally, 
mosses are anchored to the substrate—whether it is soil, rock, or roof tiles 
—by multicellular rhizoids. These structures are precursors of roots. They 
originate from the base of the gametophyte, but are not the major route for 
the absorption of water and minerals. The lack of a true root system 
explains why it is so easy to rip moss mats from a tree trunk. The moss 
lifecycle follows the pattern of alternation of generations as shown in [link]. 


Seedless Vascular Plants 


Introduction 

"We might expect... in the summer of the ‘great year,’ which we are now 
considering, that there would be a great predominance of tree-ferns and 
plants allied to the palms and arborescent grasses in the isles of the wide 
ocean, while the dicotyledenous plants and other forms now most common 
in temperate regions would almost disappear from the earth. Then might 
these genera of animals return, of which the memorials are preserved in the 
ancient rocks of our continents. The huge iguanodon might reappear in the 
woods, and the ichthyosaur in the sea, while the pterodactyle might flit 
again through umbrageous groves of tree-ferns. Coral reefs might be 
prolonged beyond the arctic circle, where the whale and narwal [sic] now 
abound. Turtles might deposit their eggs in the sand of the sea beach, where 
now the walrus sleeps, and where the seal is drifted on the ice-floe. " Sir 
Charles Lyell, Principles of Geology, (1830) 


Lyell's book, which greatly influenced scientists in the time of Darwin, 
appeared just as science was comprehending the value of the fossil record 
in reconstructing the history of life on earth. Fossilized tree-ferns from coal 
mines in Britain and North America gave hints of an ancient time of lush 
tropical forests in those regions, and how and when those forests 
disappeared was a mystery waiting to be solved. The vascular plants, 
including ferns and their allies, are the dominant and most conspicuous 
group of land plants. More than 260,000 species (including ferns, 
gymnosperms and angiosperms) represent more than 90 percent of Earth’s 
vegetation. Several evolutionary innovations explain their success and their 
ability to spread to all habitats. 

A tree-fern in New Zealand 


A modern tree-fern in the forests of New 
Zealand. This particular species is the Silver 
Fern (Cyathea dealbata), the national 
symbol of New Zealand, which appears on 
the uniforms of the national Rugby Team, 
the All Blacks. 


Bryophytes may have been successful at the transition from an aquatic 
habitat to land, but they are still dependent on water for reproduction, and 
absorb moisture and nutrients through the gametophyte surface. The lack of 
roots for absorbing water and minerals from the soil, as well as a lack of 
reinforced conducting cells, limits bryophytes to small sizes. Although they 
may survive in reasonably dry conditions, they cannot reproduce and 
expand their habitat range in the absence of water. Vascular plants, on the 
other hand, can achieve enormous heights, thus competing successfully for 
light. Photosynthetic organs become leaves, and pipe-like cells or vascular 
tissues transport water, minerals, and fixed carbon throughout the organism. 


In seedless vascular plants, the diploid sporophyte is the dominant phase of 
the lifecycle. The gametophyte is now an inconspicuous, but still 
independent, organism. Throughout plant evolution, there is an evident 
reversal of roles in the dominant phase of the lifecycle. Seedless vascular 
plants still depend on water during fertilization, as the sperm must swim on 
a layer of moisture to reach the egg. This step in reproduction explains why 
ferns and their relatives are more abundant in damp environments. 


Characteristics of Seedless Vascular Plants 

As the name implies, this group of plants lack seeds and fruit but do have 
vascular tissue. The vascular tissue xylem and phloem are used to move 
water throughout the plant and there is lignin found in the cell walls for 
structural support and for enhanced water transport efficiency. However, 
water is still necessary for sperm to swim to the egg and why many ferns 
and their relatives are found in damp environments. Lastly, the sporophyte 
is the dominant phase of the life cycle with the gametophyte being and 
inconspicuous and independent organism. 


Vascular Tissue: Xylem and Phloem 


The first fossils that show the presence of vascular tissue date to the 
Silurian period, about 430 million years ago. The simplest arrangement of 
conductive cells shows a pattern of xylem at the center surrounded by 
phloem. Xylem is the tissue responsible for the storage and long-distance 
transport of water and nutrients, as well as the transfer of water-soluble 
growth factors from the organs of synthesis to the target organs. The tissue 
consists of conducting cells, known as tracheids, and supportive filler 
tissue, called parenchyma. Xylem conductive cells incorporate the 
compound lignin into their walls, and are thus described as lignified. Lignin 
itself is a complex polymer that is impermeable to water and strengthens 
vascular tissue. With their rigid cell walls, the xylem cells provide support 
to the plant and allow it to achieve impressive heights. Tall plants have a 
selective advantage by being able to reach unfiltered sunlight and disperse 
their spores or seeds further away, thus expanding their range. By growing 
higher than other plants, tall trees cast their shadow on shorter plants and 
limit competition for water and precious nutrients in the soil. 


Phloem is the second type of vascular tissue; it transports sugars, proteins, 
and other solutes throughout the plant. Phloem cells are divided into sieve 
elements (conducting cells) and cells that support the sieve elements. 
Together, xylem and phloem tissues form the vascular system of plants. 


Roots: Support for the Plant 


Roots are not well preserved in the fossil record. Nevertheless, it seems that 
roots appeared later in evolution than vascular tissue. The development of 
an extensive network of roots represented a significant new feature of 
vascular plants. Thin rhizoids attached bryophytes to the substrate, but these 
rather flimsy filaments did not provide a strong anchor for the plant; neither 
did they absorb substantial amounts of water and nutrients. In contrast, 
roots, with their prominent vascular tissue system, transfer water and 
minerals from the soil to the rest of the plant. The extensive network of 
roots that penetrates deep into the soil to reach sources of water also 
stabilizes plants by acting as a ballast or anchor. The majority of roots 
establish a mulutalistic relationship with fungi, forming mycorrhizae, which 
benefit the plant by greatly increasing the surface area for absorption of 
water and soil minerals and nutrients. 


Leaves, Sporophylls, and Strobili 


A third adaptation marks the seedless vascular plants. Accompanying the 
prominence of the sporophyte and the development of vascular tissue, the 
evolution of true leaves improved photosynthetic efficiency. Leaves capture 
more sunlight with their increased surface area by employing more 
chloroplasts to trap light energy and convert it to chemical energy, which is 
then used to fix atmospheric carbon dioxide into carbohydrates. The 
carbohydrates are exported to the rest of the plant by the conductive cells of 
phloem tissue. 


The existence of two types of morphology suggests that leaves evolved 
independently in several groups of plants. The first type of leaf is the 
microphyll, or “little leaf,” which can be dated to 350 million years ago in 
the late Silurian. A microphyll is small and has a simple vascular system. A 
single unbranched vein—a bundle of vascular tissue made of xylem and 


phloem—truns through the center of the leaf. Microphylls may have 
originated from the flattening of lateral branches, or from sporangia that 
lost their reproductive capabilities. Microphylls are present in the club 
mosses and probably preceded the development of megaphylls, or “big 
leaves”, which are larger leaves with a pattern of branching veins. 
Megaphylls most likely appeared independently several times during the 
course of evolution. Their complex networks of veins suggest that several 
branches may have combined into a flattened organ, with the gaps between 
the branches being filled with photosynthetic tissue. 


In addition to photosynthesis, leaves play another role in the lives of plants. 
Pine cones, mature fronds of ferns, and flowers are all sporophylls—leaves 
that were modified structurally to bear sporangia. Strobili are cone-like 
structures that contain sporangia. They are prominent in conifers and are 
commonly known as pine cones. 


Ferns and Other Seedless Vascular Plants 


By the late Devonian period, plants had evolved vascular tissue, well- 
defined leaves, and root systems. With these advantages, plants increased in 
height and size. During the Carboniferous period, swamp forests of club 
mosses and horsetails—some specimens reaching heights of more than 30 
m (100 ft)—covered most of the land. These forests gave rise to the 
extensive coal deposits that gave the Carboniferous its name. In seedless 
vascular plants, the sporophyte became the dominant phase of the lifecycle. 


Water is still required for fertilization of seedless vascular plants, and most 
favor a moist environment. Modern-day seedless vascular plants include 
club mosses, horsetails, ferns, and whisk ferns. 


Phylum Lycopodiophyta: Club Mosses 


The club mosses, or phylum Lycopodiophyta, are the earliest group of 
seedless vascular plants. They dominated the landscape of the 
Carboniferous, growing into tall trees and forming large swamp forests. 
Today’s club mosses are diminutive, evergreen plants consisting of a stem 


(which may be branched) and microphylls ({link]). The phylum 
Lycopodiophyta consists of close to 1,200 species, including quillworts 
(Isoetales), club mosses (Lycopodiales), and spike mosses (Selaginellales), 
which, despite their common names, are not true mosses (bryophytes). 


Lycophytes follow the pattern of alternation of generations seen in the 
bryophytes, except that the sporophyte is the major stage of the lifecycle. 
The gametophytes do not depend on the sporophyte for nutrients. Some 
gametophytes develop underground and form mycorrhizal associations with 
fungi. In club mosses, the sporophyte gives rise to sporophylls arranged in 
strobili, cone-like structures that give the class its name. Lycophytes can be 
homosporous or heterosporous. 


In the club mosses such as 
Lycopodium clavatum, 
sporangia are arranged in 
clusters called strobili. (credit: 
Cory Zanker) 


Phylum Monilophyta: Class Equisetopsida (Horsetails) 


Horsetails, whisk ferns and ferns belong to the phylum Monilophyta, with 
horsetails placed in the Class Equisetopsida. The modern genus Equisetum 
contains the only survivors of a large and diverse group of horsetails known 
as the Arthrophyta, which produced large trees and entire swamp forests 
during the Carboniferous. The plants are usually found in damp 
environments and marshes ([link]). 


Horsetails thrive in a marsh. 
(credit: Myriam Feldman) 


The stem of a horsetail is characterized by the presence of joints or nodes, 
hence the name Arthrophyta (arthro- = "joint"; -phyta = "plant"). Leaves 
and branches come out as whorls from the evenly spaced joints. The needle- 
shaped leaves do not contribute greatly to photosynthesis, the majority of 
which takes place in the green stem ([link]). 


Thin leaves originating at 
the joints are noticeable 
on the horsetail plant. 
Horsetails were once used 
as scrubbing brushes and 
were nicknamed scouring 
brushes. (credit: Myriam 
Feldman) 


Silica collects in the epidermal cells, contributing to the stiffness of 
horsetail plants. Underground stems known as rhizomes anchor the plants to 
the ground. Modern-day horsetails are homosporous and an individual 
produces both male and female gametes. 


Phylum Monilophyta: Class Psilotopsida (Whisk Ferns) 


While most ferns form large leaves and branching roots, the whisk ferns, 
Class Psilotopsida, lack both roots and leaves. Photosynthesis takes place in 


their green stems, and small yellow knobs form at the tip of the branch stem 
and contain the sporangia. 


The whisk fern Psilotum nudum 
has conspicuous green stems 
with knob-shaped sporangia. 
(credit: Forest & Kim Starr) 


Phylum Monilophyta: Class Psilotopsida (Ferns) 


Ferns are the most readily recognizable seedless vascular plants and are 
considered the most advanced seedless vascular plants because they display 
characteristics commonly observed in seed plants. More than 20,000 
species of ferns live in environments ranging from tropics to temperate 
forests. Although some species survive in dry environments, most ferns are 
restricted to moist, shaded places. Ferns made their appearance in the fossil 
record during the Devonian period and expanded during the Carboniferous. 


The dominant stage of the lifecycle of a fern is the sporophyte, which 
consists of large compound leaves called fronds. Fronds fulfill a double 
role; they are photosynthetic organs that also carry reproductive organs. The 


stem may be buried underground as a rhizome, from which adventitious 
roots grow to absorb water and nutrients from the soil; or, they may grow 
above ground as a trunk in tree ferns ([link]). Adventitious organs are those 
that grow in unusual places, such as roots growing from the side of a stem. 


Some specimens of this short 
tree-fern species can grow very 
tall. (credit: Adrian Pingstone) 


The tip of a developing fern frond is rolled into a crozier, or fiddlehead 
({link]Ja and [link]b). Fiddleheads unroll as the frond develops. 


Croziers, or fiddleheads, are the tips of 
fern fronds. (credit a: modification of 


work by Cory Zanker; credit b: 
modification of work by Myriam 
Feldman) 


The lifecycle of a fern is depicted in [link]. 


Fern Life Cycle 


This life cycle of a fern shows alternation of generations with a 
dominant sporophyte stage. Work by Eva Horne and Robert A. Bear 


Most ferns produce a single type of spore and are therefore homosporous. 
The diploid sporophyte is the most conspicuous stage of the lifecycle. On 
the underside of its mature fronds, sori (singular, sorus) form as small 
clusters where sporangia develop ([link]). 


Sori appear as small bumps on the 
underside of a fern frond. (credit: 
Myriam Feldman) 


Inside the sori, spores are produced by meiosis and released into the air. 
Those that land on a suitable substrate germinate and form a heart-shaped 
gametophyte, which is attached to the ground by thin filamentous rhizoids 
([link]). 


Sporophyte 


ee Gametophyte hm 


Shown here are a young 
sporophyte (upper part of image) 
and a heart-shaped gametophyte 

(bottom part of image). (credit: 
modification of work by 
"VImastra"/Wikimedia Commons) 


The inconspicuous gametophyte harbors both sex gametangia. Flagellated 
sperm released from the antheridium swim on a wet surface to the 
archegonium, where the egg is fertilized. The newly formed zygote grows 
into the next generation sporophyte. 


The Importance of Bryophytes and Seedless Vascular Plants 


Mosses and liverworts are often the first macroscopic organisms to colonize 
an area, both in a primary succession—where bare land is settled for the 
first time by living organisms—or in a secondary succession, where soil 
remains intact after a catastrophic event wipes out many existing species. 
Their spores are carried by the wind, birds, or insects. Once mosses and 
liverworts are established, they provide food and shelter for other species. 
In a hostile environment, like the tundra where the soil is frozen, 
bryophytes grow well because they do not have roots and can dry and 
rehydrate rapidly once water is again available. Mosses are at the base of 
the food chain in the tundra biome. Many species—from small insects to 
musk oxen and reindeer—depend on mosses for food. In turn, predators 
feed on the herbivores, which are the primary consumers. Some reports 
indicate that bryophytes make the soil more amenable to colonization by 
other plants. Because they establish symbiotic relationships with nitrogen- 
fixing cyanobacteria, mosses replenish the soil with nitrogen. 


At the end of the nineteenth century, scientists observed that lichens and 
mosses were becoming increasingly rare in urban and suburban areas. Since 
bryophytes have neither a root system for absorption of water and nutrients, 
nor a cuticle layer that protects them from desiccation, pollutants in 


rainwater readily penetrate their tissues; they absorb moisture and nutrients 
through their entire exposed surfaces. Therefore, pollutants dissolved in 
rainwater penetrate plant tissues readily and have a larger impact on mosses 
than on other plants. The disappearance of mosses can be considered a 
bioindicator for the level of pollution in the environment. 


Ferns contribute to the environment by promoting the weathering of rock, 
accelerating the formation of topsoil, and slowing down erosion by 
spreading rhizomes in the soil. The water ferns of the genus Azolla harbor 
nitrogen-fixing cyanobacteria and restore this important nutrient to aquatic 
habitats. 


Seedless plants have historically played a role in human life through use as 
tools, fuel, and medicine. Dried peat moss, Sphagnum, is commonly used as 
fuel in some parts of Europe and is considered a renewable resource. 
Sphagnum bogs ([link]) are cultivated with cranberry and blueberry bushes. 
The ability of Sphagnum to hold moisture makes the moss a common soil 
conditioner. Florists use blocks of Sphagnum to maintain moisture for floral 
arrangements. 


Sphagnum acutifolium is dried 
peat moss and can be used as 
fuel. (credit: Ken Goulding) 


The attractive fronds of ferns make them a favorite ornamental plant. 
Because they thrive in low light, they are well suited as house plants. More 
importantly, fiddleheads are a traditional spring food of Native Americans 
in the Pacific Northwest, and are popular as a side dish in French cuisine. 
The licorice fern, Polypodium glycyrrhiza, is part of the diet of the Pacific 
Northwest coastal tribes, owing in part to the sweetness of its rhizomes. It 
has a faint licorice taste and serves as a sweetener. The rhizome is also 
valued by Native Americans for its medicinal properties and is used as a 
remedy for sore throat. 


By far the greatest impact of seedless vascular plants on human life, 
however, comes from their extinct progenitors. The tall club mosses, 
horsetails, and tree-like ferns that flourished in the swampy forests of the 
Carboniferous period gave rise to large deposits of coal throughout the 
world. Coal provided an abundant source of energy during the Industrial 
Revolution, which had tremendous consequences on human societies, 
including rapid technological progress and growth of large cities, as well as 
the degradation of the environment. Coal is still a prime source of energy 
and also a major contributor to global warming. 


Evolution of Seed Plants 


Introduction 

" T was aware of Darwin's views fourteen years before I adopted them and I 
have done so solely and entirely from an independent study of the plants 
themselves. " Sir Joseph Dalton Hooker, letter to E.H. Harvey, in L. Huxley, 
Life and Letters of Sir Joseph Dalton Hooker (1918) 


The evolution of plants is indeed well-understood, and Hooker's recognition 
of the usefulness of evolutionary theory in understanding plant biology was 
correct. The first plants to colonize land were most likely closely related to 
modern day mosses (bryophytes) and are thought to have appeared about 
500 million years ago, based on fossil and DNA sequence evidence. They 
were followed by liverworts (also bryophytes) and primitive vascular plants 
—the pterophytes—from which modern ferns are derived. Like 
gymnosperms and angiosperms, the life cycle of bryophytes and 
pterophytes is characterized by the alternation of generations. What sets 
bryophytes and pterophytes apart from gymnosperms and angiosperms is 
their reproductive requirement for water. The completion of the bryophyte 
and pterophyte life cycle requires water because the male gametophyte 
releases sperm, which must swim—propelled by their flagella—to reach 
and fertilize the female gamete or egg. After fertilization, the zygote 
matures and grows into a sporophyte, which in turn will form sporangia or 
"spore vessels." In the sporangia, mother cells undergo meiosis and produce 
the haploid spores. Release of spores in a suitable environment will lead to 
germination and a new generation of gametophytes. 


In seed plants, the evolutionary trend led to a dominant sporophyte 
generation, and at the same time, a systematic reduction in the size of the 
gametophyte: from a conspicuous structure to a microscopic cluster of cells 
enclosed in the tissues of the sporophyte. The gametophyte is thus 
dependent on the sporophyte for shelter and nutrition. Whereas lower 
vascular plants, such as club mosses and ferns, are mostly homosporous 
(produce only one type of spore), all seed plants are heterosporous. They 
form two types of spores: megaspores (female) and microspores (male). 
Megaspores develop into female gametophytes that produce eggs, and 
microspores mature into male gametophytes that generate sperm. Because 


the gametophytes mature within the sporophyte, they are not free-living, as 
are the gametophytes of other seedless vascular plants. Heterosporous 
seedless plants are seen as the evolutionary forerunners of seed plants. 


Seeds and pollen—two critical adaptations to drought, and to reproduction 
that doesn’t require water—distinguish seed plants from other (seedless) 
vascular plants. Both adaptations were required for the colonization of land 
begun by the bryophytes and their ancestors. Fossils place the earliest 
distinct seed plants at about 350 million years ago. The first reliable record 
of gymnosperms dates their appearance to the late Paleozoic, about 319 
million years ago ([link]). Gymnosperms were preceded by 
progymnosperms, the first naked seed plants, which arose about 380 million 
years ago. Progymnosperms were a transitional group of plants that 
superficially resembled conifers (cone bearers) because they produced 
wood from the secondary growth of vascular tissues; however, they still 
reproduced like ferns, releasing spores into the environment. Gymnosperms 
dominated the landscape in the early and middle Mesozoic era. 
Angiosperms surpassed gymnosperms by about 100 million years ago in the 
late Mesozoic era, and today are the most abundant plant group in most 
terrestrial biomes. 


Flowers and Fruits 
Angiosperms 


Seeds Gnetophytes 
Conifers 
Vascular Gymnosperms 


Ginkgos 


Tissue Cycads 


Whisk ferns | Vascular 


True ferns 
Horsetails Seedless 
Club mosses 


Land 
Plants 


Mosses 
Hornworts Bryophytes 


Liverworts 


500 400 300 200 100 0 


Time (millions of year ago) 


Phylogeny of the land plants with the major adaptation for living on 
land. Note the geological eras along the bottom. Work by Robert A. 


Bear 


Pollen and seed were adaptations that allowed seed plants to break their 
dependence on water for reproduction and development of the embryo, and 
to conquer dry land. The pollen grains are the male gametophytes, which 
contain the sperm (gametes) of the plant. The small haploid (1N) cells are 
encased in a protective coat that prevents desiccation (drying out) and 
mechanical damage. Pollen grains can travel far from their original 
sporophyte, spreading the plant’s genes. The seed offers the embryo 
protection, nourishment, and a mechanism to maintain dormancy for tens or 
even thousands of years, ensuring germination can occur when growth 
conditions are optimal. Seeds therefore allow plants to disperse the next 
generation through both space and time. With such evolutionary 
advantages, seed plants have become the most successful and familiar 
group of plants, in part because of their size and striking appearance. 


Evolution of Gymnosperms 


The fossil plant Elkinsia polymorpha, a "seed fern" from the Devonian 
period—about 400 million years ago—is considered the earliest seed plant 
known to date. Seed ferns ((link]) produced seeds along their branches 
without specialized structures. What makes them the first true seed plants is 
that they developed structures to enclose and protect the ovule—the female 
gametophyte and associated tissues—which develops into a seed upon 
fertilization. Seed plants resembling modern tree ferns became more 
numerous and diverse in the coal swamps of the Carboniferous period. 


This fossilized leaf is from 
Glossopteris, a seed fern that thrived 
during the Permian age (290— 
240 million years ago). (credit: D.L. 
Schmidt, USGS) 


Fossil records indicate the first gymnosperms (progymnosperms) most 
likely originated in the Paleozoic era, during the middle Devonian period: 
about 390 million years ago. Following the wet Mississippian and 
Pennsylvanian periods, which were dominated by giant fern trees, the 
Permian period was dry. This gave a reproductive edge to seed plants, 
which are better adapted to survive dry spells. The Ginkgoales, a group of 
gymnosperms with only one surviving species— Gingko biloba—were the 
first gymnosperms to appear during the lower Jurassic. Gymnosperms 
expanded in the Mesozoic era (about 240 million years ago), supplanting 
ferns in the landscape, and reaching their greatest diversity during this time. 
The Jurassic period was as much the age of the cycads (palm-tree-like 
gymnosperms) as the age of the dinosaurs. Gingkoales and more familiar 
conifers also dotted the landscape. Although angiosperms (flowering plants) 
are the major form of plant life in most biomes, gymnosperms still 
dominate some ecosystems, such as the taiga (boreal forests) and the alpine 
forests at higher mountain elevations ({link]) because of their adaptation to 
cold and dry growth conditions. 


This boreal forest (taiga) has low- 
lying plants and conifer trees. 
(credit: L.B. Brubaker, NOAA) 


Seeds and Pollen as an Evolutionary Adaptation to Dry Land 


Unlike bryophyte and fern spores (which are haploid cells dependent on 
moisture for rapid development of gametophytes), seeds contain a diploid 
embryo that will germinate into a sporophyte. Storage tissue to sustain 
growth and a protective coat give seeds their superior evolutionary 
advantage. Several layers of hardened tissue prevent desiccation, and free 
reproduction from the need for a constant supply of water. Furthermore, 
seeds remain in a state of dormancy—induced by desiccation and the 
hormone abscisic acid—until conditions for growth become favorable. 
Whether blown by the wind, floating on water, or carried away by animals, 
seeds are scattered in an expanding geographic range, thus avoiding 
competition with the parent plant. 


Pollen grains ({link]) are male gametophytes and are carried by wind, water, 
or a pollinator. The whole structure is protected from desiccation and can 
reach the female organs without dependence on water. Male gametes reach 
female gametophyte and the egg cell though a pollen tube: an extension of a 
cell within the pollen grain. The sperm of modern gymnosperms lack 


flagella, but in cycads and the Gingko, the sperm still possess flagella that 
allow them to swim down the pollen tube to the female gamete; however, 
they are enclosed in a pollen grain. 


< ‘ 
\ 
ie 
Fy} 
Cs bor 
be 


This fossilized pollen is from 
a Buckbean fen core found in 
Yellowstone National Park, 
Wyoming. The pollen is 
magnified 1,054 times. 
(credit: R.G. Baker, USGS; 
scale-bar data from Matt 
Russell) 


10m 


Evolution of Angiosperms 


Undisputed fossil records place the massive appearance and diversification 
of angiosperms in the middle to late Mesozoic era. Angiosperms (“seed in a 
vessel”) produce a flower containing male and/or female reproductive 
structures. Fossil evidence ([link]) indicates that flowering plants first 
appeared in the Lower Cretaceous, about 125 million years ago, and were 
rapidly diversifying by the Middle Cretaceous, about 100 million years ago. 
Earlier traces of angiosperms are scarce. Fossilized pollen recovered from 
Jurassic geological material has been attributed to angiosperms. A few early 
Cretaceous rocks show clear imprints of leaves resembling angiosperm 
leaves. By the mid-Cretaceous, a staggering number of diverse flowering 
plants crowd the fossil record. The same geological period is also marked 
by the appearance of many modern groups of insects, including pollinating 
insects that played a key role in ecology and the evolution of flowering 
plants. 


Although several hypotheses have been offered to explain this sudden 
profusion and variety of flowering plants, none have garnered the consensus 
of paleobotanists (scientists who study ancient plants). New data in 
comparative genomics and paleobotany have, however, shed some light on 
the evolution of angiosperms. The two adaptations of flowers and fruit 
represent an improved reproductive strategy that served to protect the 
embryo, while increasing genetic variability and range. Angiosperms did 
not evolve from gymnosperms, but the groups do share a common ancestor 
({link]). 


The most primitive living angiosperm is considered to be Amborella 
trichopoda, a small plant native to the rainforest of New Caledonia, an 
island in the South Pacific. Analysis of the genome of A. trichopoda has 
shown that it is related to all existing flowering plants and belongs to the 
oldest confirmed branch of the angiosperm family tree. A few other 
angiosperm groups called basal angiosperms, are viewed as primitive 
because they branched off early from the phylogenetic tree. Most modern 
angiosperms are Classified as either monocots or eudicots, based on the 
structure of their leaves and embryos. Basal angiosperms, such as water 
lilies, are considered more primitive because they share morphological 
traits with both monocots and eudicots. 


This leaf imprint shows 
a Ficus speciosissima, 
an angiosperm that 
flourished during the 
Cretaceous period. 
(credit: W. T. Lee, 
USGS) 


Flowers and Fruits as an Evolutionary Adaptation 


Angiosperms produce their gametes in separate organs, which are usually 
housed in a flower. Both fertilization and embryo development take place 
inside an anatomical structure that provides a stable system of sexual 
reproduction largely sheltered from environmental fluctuations. Flowering 
plants are the most diverse phylum on Earth after insects (Arthropoda); 
flowers come in a bewildering array of sizes, shapes, colors, smells, and 
arrangements. Most flowers have a mutualistic pollinator, with the 
distinctive features of flowers reflecting the nature of the pollination agent. 


The relationship between pollinator and flower characteristics is one of the 
great examples of coevolution. 


Following fertilization of the egg, the ovule grows into a seed. The 
surrounding tissues of the ovary thicken, developing into a fruit that will 
protect the seed and often ensure its dispersal over a wide geographic range. 
Not all fruits develop from an ovary; such structures are “false fruits.” Like 
flowers, fruit can vary tremendously in appearance, size, smell, and taste. 
Tomatoes, walnut shells and avocados are all examples of fruit. As with 
pollen and seeds, fruits also act as agents of dispersal. Some may be carried 
away by the wind. Many attract animals that will eat the fruit and pass the 
seeds through their digestive systems, then deposit the seeds in another 
location. Cockleburs are covered with stiff, hooked spines that can hook 
into fur (or clothing) and hitch a ride on an animal for long distances. The 
cockleburs that clung to the velvet trousers of an enterprising Swiss hiker, 
George de Mestral, inspired his invention of the loop and hook fastener he 
named Velcro. 


Gymnosperms 


Introduction 
" Tt took more than three thousand years to make some of the trees in these 
westem woods ... Through all the wonderful, eventful centuries since 
Christ's time—and long before that—God has cared for these trees, saved 
them from drought, disease, avalanches, and a thousand straining, leveling 
tempests and floods; but he cannot save them from fools." John Muir, in 
"The American Forests", Atlantic Monthly (Aug 1897) 

Giant Sequoia — 


The Grizzly Giant, a Giant Sequoia 
(Sequoiadendron giganteum) in the 
Mariposa Grove of Yosemite National 
Park. John Muir and others petitioned the 


US Congress, resulting in the creation of 
Yosemite and Sequoia National Parks in 
1890. Photo by David A. Rintoul. 


The redwood trees and Douglas firs referred to in Muir's quote are indeed 
ancient, and among the largest living things on the planet. They are 
members of the group we call gymnosperms, meaning “naked seeds,” 
which are a diverse group of seed plants and are paraphyletic. Paraphyletic 
groups are those in which not all members are descendants of a single 
common ancestor. Gymnosperm characteristics include naked seeds (not 
enclosed in an ovary), separate female and male gametes, pollination by 
wind, and tracheids (which transport water and solutes in the vascular 
system). 


Gymnosperm seeds are not enclosed in an ovary (they are "naked"); rather, 
they are exposed on cones or modified leaves. Gymnosperms were the 
dominant phylum in the Mesozoic era. They are adapted to live where fresh 
water is scarce during part of the year, or in the nitrogen-poor soil of a bog. 
Therefore, they are still the prominent phylum in the coniferous biome or 
taiga, where the evergreen conifers have a selective advantage in cold and 
dry weather. Evergreen conifers continue low levels of photosynthesis 
during the cold months, and are ready to take advantage of the first sunny 
days of spring. One disadvantage is that conifers are more susceptible than 
deciduous trees to infestations because conifers do not lose their leaves all 
at once. They cannot, therefore, shed parasites and restart with a fresh 
supply of leaves in spring. 


The life cycle of a gymnosperm involves alternation of generations, with a 
dominant sporophyte and reduced gametophytes that resides within the 
sporophyte. All gymnosperms are heterosporous. The male and female 
reproductive organs can form in cones (strobili). Male and female sporangia 
are produced either on the same plant, described as monoecious (“one 
home”), or on separate plants, referred to as dioecious (“two homes”) 
plants. The life cycle of a conifer will serve as our example of reproduction 
in gymnosperms. 


Life Cycle of a Conifer 


Pine trees are conifers (cone bearing) and carry both male and female 
sporophylls on the same mature sporophyte. Therefore, they are 
monoecious plants. Like all gymnosperms, pines are heterosporous and 
generate two different types of spores: male microspores and female 
megaspores. In the male or staminate cones, the microsporocytes give rise 
to pollen grains by meiosis. In the spring, large amounts of yellow pollen 
are released and carried by the wind. Some gametophytes will land on a 
female cone. Pollination is defined as the initiation of pollen tube growth. 
The pollen tube develops slowly, and the generative cell in the pollen grain 
divides into two haploid sperm cells by mitosis. At fertilization, one of the 
sperm cells will finally unite its haploid nucleus with the haploid nucleus of 
a haploid egg cell. 


Female cones contain two ovules per scale. One megaspore mother cell, or 
megasporocyte, undergoes meiosis in each ovule. Three of the four cells 
break down; only a single surviving cell will develop into a female 
multicellular gametophyte, which encloses one or more archegonia (an 
archegonium is a reproductive organ that contains a single large egg). Upon 
fertilization, the resulting diploid zygote will give rise to the embryo, which 
is enclosed in a seed coat of tissue from the parent plant. Fertilization and 
seed development is a long process in pine trees: it may take up to two 
years after pollination. The seed that is formed contains three generations of 
tissues: the seed coat that originates from the sporophyte tissue, the 
gametophyte that will provide nutrients, and the embryo itself. 


[link] illustrates the life cycle of a conifer. The sporophyte (2N) phase is the 
longest phase in the life of a gymnosperm. The gametophytes (1N)— 
microspores and megaspores—are reduced in size. It may take more than 
year between pollination and fertilization while the pollen tube grows 
towards the megasporocyte (2N), which undergoes meiosis into 
megaspores. The megaspores will mature into female gametophytes that 
then produce eggs (1N). 


Gymnosperm Life Cycle 


ee ere ~ ee §,.& Male Gametophyte (Pollen) 
oe Se 
Microspores Mitosis © Pollination so” 


P'S a7 


This image shows the life cycle of a conifer. Pollen from male cones 
blows up into upper branches, where it fertilizes female cones. Work 
by Eva Horne and Robert A. Bear 


Diversity of Gymnosperms 


Modern gymnosperms are classified into four phyla. Coniferophyta, 
Cycadophyta, and Ginkgophyta are similar in their production of secondary 
cambium (cells that generate the vascular system of the trunk or stem and 
are partially specialized for water transportation) and their pattern of seed 
development. However, the three phyla are not closely related 


phylogenetically to each other. Gnetophyta are considered the closest group 
to angiosperms because they produce true xylem tissue. 


Conifers (Coniferophyta) 


Conifers are the dominant phylum of gymnosperms, with the most variety 
of species ([link]). Most are typically tall trees that usually bear scale-like 
or needle-like leaves. Water evaporation from leaves is reduced by their thin 
shape and the thick cuticle. Snow slides easily off needle-shaped leaves, 
keeping the load light and decreasing breaking of branches. Adaptations to 
cold and dry weather explain the predominance of conifers at high altitudes 
and in cold climates. Conifers include familiar evergreen trees such as 
pines, spruces, firs, cedars, sequoias, and yews. A few species are 
deciduous and lose their leaves in fall. The European larch and the tamarack 
are examples of deciduous conifers ([link]d). Many coniferous trees are 
harvested for paper pulp and timber. The wood of conifers is more primitive 
than the wood of angiosperms; it contains tracheids, but no vessel elements, 
and is therefore referred to as “soft wood.” 


Conifers are the dominant form of vegetation 
in cold or arid environments and at high 
altitudes. Shown here are the (a) evergreen 
spruce Picea sp., (b) juniper Juniperus sp., (c) 
coast redwood Sequoia sempervirens, which is 
a deciduous gymnosperm, and (d) the tamarack 
Larix larcinia. Notice the yellow leaves of the 
tamarack. (credit a: modification of work by 
Rosendahl; credit b: modification of work by 
Alan Levine; credit c: modification of work by 
Wendy McCormic; credit d: modification of 
work by Micky Zlimen) 


Cycads 


Cycads thrive in mild climates, and are often mistaken for palms because of 
the shape of their large, compound leaves. Cycads bear large cones ((link]), 
and may be pollinated by beetles rather than wind: unusual for a 
gymnosperm. They dominated the landscape during the age of dinosaurs in 
the Mesozoic, but only a hundred or so species persisted to modern times. 
They face possible extinction, and several species are protected through 
international conventions. Because of their attractive shape, they are often 
used as ornamental plants in gardens in the tropics and subtropics. 


This Encephalartos ferox cycad 
has large cones and broad, fern- 
like leaves. (credit: Wendy Cutler) 


Gingkophytes 


The single surviving species of Gingkophytes is the Gingko biloba ({link)). 
Its fan-shaped leaves—unique among seed plants because they feature a 
dichotomous venation pattern—turn yellow in autumn and fall from the 
tree. For centuries, G. biloba was cultivated by Chinese Buddhist monks in 
monasteries, which ensured its preservation. It is planted in public spaces 


because it is unusually resistant to pollution. Male and female organs are 
produced on separate plants. Typically, gardeners plant only male trees 
because the seeds produced by the female plant have an off-putting smell of 
rancid butter. 


Th 30, 


This plate from the 1870 
book Flora Japonica, Sectio 
Prima (Tafelband) depicts the 
leaves and fruit of Gingko 
biloba, as drawn by Philipp 
Franz von Siebold and Joseph 
Gerhard Zuccarini. 


Gnetophytes 


Gnetophytes are the closest relative to modern angiosperms, and include 
three dissimilar genera of plants: Ephedra, Gnetum, and Welwitschia 
({link]). Like angiosperms, they have broad leaves. In tropical and 
subtropical zones, gnetophytes are vines or small shrubs. Ephedra occurs in 
dry areas of the West Coast of the United States and Mexico. Ephedra’s 
small, scale-like leaves are the source of the compound ephedrine, which is 
used in medicine as a potent decongestant. Because ephedrine is similar to 
amphetamines, both in chemical structure and neurological effects, its use is 
restricted to prescription drugs. Like angiosperms, but unlike other 
gymnosperms, all gnetophytes possess vessel elements in their xylem. 


(a) Ephedra (b) Gnetum (c) Welwitschia 


(a) Ephedra viridis, known by the common name Mormon tea, 
grows on the West Coast of the United States and Mexico. (b) 
Gnetum gnemon grows in Malaysia. (c) The large Welwitschia 
mirabilis can be found in the Namibian desert. (credit a: 
modification of work by USDA; credit b: modification of work 
by Malcolm Manners; credit c: modification of work by Derek 
Keats) 


Angiosperms 


Introduction 

"The ginkgo tree is from the era of dinosaurs, but while the dinosaur has 
been extinguished, the modern ginkgo has not changed. After the atomic 
bomb in Hiroshima, the ginkgo was the first tree that came up. It’s 
amazing." Koji Nakanishi, organic chemist (2013) 


From their humble and still obscure beginning during the early Jurassic 
period, the angiosperms—or flowering plants—have evolved to dominate 
most terrestrial ecosystems ([link]). With more than 250,000 species, the 
angiosperm phylum (Anthophyta) is second only to insects in terms of 
diversification. 


4 


These flowers grow in a botanical 
garden border in Bellevue, WA. 
Flowering plants dominate terrestrial 
landscapes. The vivid colors of 
flowers are an adaptation to 
pollination by animals such as insects 
and birds. (credit: Myriam Feldman) 


The success of angiosperms is due to two novel reproductive structures: 
flowers and fruit. The function of the flower is to ensure pollination. 


Flowers also provide protection for the ovule and developing embryo inside 
a receptacle. The function of the fruit is seed dispersal. They also protect 
the developing seed. Different fruit structures or tissues on fruit—such as 
sweet flesh, wings, parachutes, or spines that grab—reflect the dispersal 
strategies that help spread seeds. 


Flowers 


Flowers are modified leaves, or sporophylls, organized around a central 
stalk. Although they vary greatly in appearance, all flowers contain the 
Same structures: sepals, petals, carpels, and stamens. The receptacle 
attaches the flower to the plant. A whorl of sepals (collectively called the 
calyx) is located at the base of the peduncle (stem of the flower) and 
encloses the unopened floral bud. Sepals are usually photosynthetic organs, 
although there are some exceptions. For example, the corolla in lilies and 
tulips consists of three sepals and three petals that look virtually identical. 
Petals, collectively the corolla, are located inside the whorl of sepals and 
often display vivid colors to attract pollinators. Flowers pollinated by wind 
are usually small, feathery, and visually inconspicuous. The sexual organs 
(carpels and stamens) are located at the center of the flower. 


As illustrated in [link], styles, stigmas, and ovules constitute the female 
organ: the carpel. Flower structure is very diverse, and carpels may be 
singular, multiple, or fused. Multiple fused carpels comprise a pistil. The 
megaspores and the female gametophytes are produced and protected by the 
thick tissues of the carpel. A long, thin structure called a style leads from 
the sticky stigma, where pollen is deposited, to the ovary, enclosed in the 
carpel. The ovary houses one or more ovules, each of which will develop 
into a seed upon fertilization. The male reproductive organs, the stamens, 
surround the central carpel. Stamens are composed of a thin stalk called a 
filament and a sac-like structure called the anther. The filament supports 
the anther, where the microspores are produced by meiosis and develop 
into pollen grains. 


Stamens 


Petal 


Flower 
Corolla (composed of petals) 
Calyx (composed of sepals) 


This image depicts the structure of a 
perfect flower. Perfect flowers produce 
both male and female floral organs. The 

flower shown has only one carpel, but 
some flowers have a cluster of carpels. 

Together, all the carpels make up the 
pistil. (credit: modification of work by 

Mariana Ruiz Villareal) 


Fruit 


As the seed develops, the walls of the ovary thicken and form the fruit. The 
seed forms in an ovary, which also enlarges as the seeds grow. In botany, a 
fertilized and fully grown, ripened ovary is a fruit. Many foods commonly 
called vegetables are actually fruit. Eggplants, zucchini, string beans, and 
bell peppers are all technically fruit because they contain seeds and are 
derived from the thick ovary tissue. Acorns (a nut), and winged maple 


whirligigs (whose botanical name is samara) are also fruit. Botanists 
classify fruit into more than two dozen different categories, only a few of 
which are actually fleshy and sweet. 


Mature fruit can be fleshy or dry. Fleshy fruit include the familiar berries, 
peaches, apples, grapes, and tomatoes. Rice, wheat, and nuts are examples 
of dry fruit. Another distinction is that not all fruits are derived from the 
ovary. For instance, strawberries are derived from the receptacle and in 
apples the receptacle forms the pericarp or the fleshy part. Some fruits are 
derived from separate ovaries in a single flower, such as the raspberry. 
Other fruits, such as the pineapple, form from clusters of flowers. 
Additionally, some fruits, like watermelon and orange, have rinds. 
Regardless of how they are formed, fruits are an agent of seed dispersal. 
The variety of shapes and characteristics reflect the mode of dispersal. 
Wind carries the light dry fruit of trees and dandelions. Water transports 
floating coconuts. Some fruits attract herbivores with color or perfume, or 
as food. Once eaten, tough, undigested seeds are dispersed through the 
herbivore’s feces. Other fruits have burs and hooks to cling to fur and hitch 
rides on animals. 


The Life Cycle of an Angiosperm 


The sporophyte phase is the main phase of an angiosperm’s life cycle 
({link]). Like gymnosperms, angiosperms are heterosporous. Therefore, 
they generate microspores, which will generate pollen grains as the male 
gametophytes, and megaspores, which will form an ovule that contains 
female gametophytes. Inside the anthers’ microsporangia, male 
gametophytes divide by meiosis to generate haploid microspores, which, in 
turn, undergo mitosis and give rise to pollen grains. Each pollen grain 
contains two cells: one generative cell that will divide into two sperm and a 
second cell that will become the pollen tube cell. 


Note: 


Angiosperm Life Cycle 


R a fed 
Tr yy Fer 


(5D) a. 


i 
f' 


The life cycle of an angiosperm is shown. Anthers and carpels are 
structures that shelter the actual gametophytes: the pollen grain and 
embryo sac. Work by Eva Horne and Robert A. Bear 


Within the ovule, sheltered within the ovary of the carpel, a cell undergoes 
meiosis, generating four megaspores—three small and one large. Only the 
large megaspore survives; it divides to produce the female gametophyte. 
The megaspore divides three times to form an eight-cell stage. Three of 
these cells migrate to each pole of the embryo sac while two come to the 
equator. These two cells will fuse to form one central cell with two haploid 


polar nuclei. The two cells closest to the egg are called synergids; the three 
cells on the opposite end of the gametophyte are called antipodals. 


Pollen grains are the male gametophytes. When a pollen grain reaches the 
stigma, a pollen tube extends from the grain, grows down the style, and 
enters through the micropyle: an opening in the outer covering of the ovule. 
Two sperm cells travel down this tube and enter the ovule. 


A double fertilization event then occurs. One sperm combines with the egg, 
forming a diploid zygote—the future embryo. The other sperm fuses with 
the two polar nuclei, forming a triploid (3n) cell that will develop into the 
endosperm, which is tissue that serves as a food reserve. The zygote 
develops into an embryo with a radicle, or small root, and one (monocot) or 
two (dicot) leaf-like organs called cotyledons. This difference in the number 
of embryonic leaves is the basis for the two major groups of angiosperms: 
the monocots and the eudicots. Seed food reserves are stored outside the 
embryo, in the form of complex carbohydrates, lipids, or proteins. The 
cotyledons serve as conduits to transmit the broken-down food reserves 
from their storage site inside the seed to the developing embryo. The seed 
consists of a toughened layer of integuments (the seed coat), the endosperm 
with food reserves, and at the center, the well-protected embryo. 


Most flowers are monoecious, which means that they carry both stamens 
and carpels. Monoecious flowers are also known as “perfect” flowers 
because they contain both types of sex organs. However, only a few species 
self-pollinate. Both anatomical and environmental barriers promote 
pollination between different individuals (cross-pollination) mediated by a 
physical agent (wind or water), or an animal, such as an insect or bird. 
Cross-pollination increases genetic diversity in a species. 


Diversity of Angiosperms 


Angiosperms are classified in a single phylum: the Anthophyta. Modern 
angiosperms appear to be a monophyletic group, which means that they 
originate from a single ancestor. Flowering plants are divided into two 
major groups, according to the structure of the cotyledons, pollen grains, 
and other structures. Monocots include grasses and lilies, and eudicots 


form a polyphyletic group. Basal angiosperms are a group of plants that 
are believed to have branched off before the separation into monocots and 
eudicots because they exhibit traits from both groups. They are categorized 
separately in many classification schemes. The Magnoliidae (magnolia 
trees, laurels, and water lilies) and the Piperaceae (peppers) belong to the 
basal angiosperm group. 


Basal Angiosperms 


The Magnoliidae are represented by the magnolias: tall trees bearing large, 
fragrant flowers that have many parts and are considered archaic ({link]d). 
Laurel trees produce fragrant leaves and small, inconspicuous flowers. The 
Laurales grow mostly in warmer climates and are small trees and shrubs. 
Familiar plants in this group include the bay laurel, cinnamon, spice bush 
({link]a), and avocado tree. The Nymphaeales are comprised of the water 
lilies, lotus ({link]c), and similar plants; all species thrive in freshwater 
biomes, and have leaves that float on the water surface or grow underwater. 
Water lilies are particularly prized by gardeners, and have graced ponds and 
pools for thousands of years. The Piperales are a group of herbs, shrubs, 
and small trees that grow in the tropical climates. They have small flowers 
without petals that are tightly arranged in long spikes. Many species are the 
source of prized fragrance or spices, for example the berries of Piper 
nigrum ((link]b) are the familiar black peppercorns that are used to flavor 
many dishes. 


The (a) common spicebush belongs to 
the Laurales, the same family as 
cinnamon and bay laurel. The fruit of 
(b) the Piper nigrum plant is black 
pepper, the main product that was 
traded along spice routes. Notice the 
small, unobtrusive, clustered flowers. 
(c) Lotus flowers, Nelumbo nucifera, 
have been cultivated since ancient 
times for their ornamental value; the 
root of the lotus flower is eaten as a 
vegetable. The red seeds of (d) a 
magnolia tree, characteristic of the 
final stage, are just starting to appear. 
(credit a: modification of work by 
Cory Zanker; credit b: modification 
of work by Franz Eugen Kohler; 
credit c: modification of work by 
"berduchwal"/Flickr; credit d: 


modification of work by 
"Coastside2"/Wikimedia Commons). 


Monocots 


Plants in the monocot group are primarily identified as such by the presence 
of a single cotyledon in the seedling. Other anatomical features shared by 
monocots include veins that run parallel to the length of the leaves, and 
flower parts that are arranged in a three- or six-fold symmetry. In monocots, 
the vascular tissue is scattered in the stem. True woody tissue is rarely 
found in monocots. In palm trees, vascular and parenchyma tissues 
produced by the primary and secondary thickening meristems form the 
trunk. The pollen from the first angiosperms was monosulcate, containing a 
single furrow or pore through the outer layer. This feature is still seen in the 
modern monocots. Vascular tissue of the stem is not arranged in any 
particular pattern. The root system is mostly adventitious and unusually 
positioned, with no major tap root. The monocots include familiar plants 
such as the true lilies (which are at the origin of their alternate name of 
Liliopsida), orchids, grasses, and palms. Many important crops are 
monocots, such as rice and other cereals, corn, sugar cane, and tropical 
fruits like bananas and pineapples ([link]). 


Monocots 


(a) Rice (b) Wheat (c) Bananas 


Dicots 


d) Cabbage ‘e) Beans Peaches 
9) 


The world’s major crops are flowering plants. (a) 
Rice, (b) wheat, and (c) bananas are monocots, while 
(d) cabbage, (e) beans, and (f) peaches are eudicots. 
(credit a: modification of work by David Nance, 
USDA ARS; credit b, c: modification of work by 
Rosendahl; credit d: modification of work by Bill 
Tarpenning, USDA; credit e: modification of work by 
Scott Bauer, USDA ARS; credit f: modification of 
work by Keith Weller, USDA) 


Eudicots 


Eudicots, or true dicots, are characterized by the presence of two cotyledons 
in the developing shoot. Veins form a network in leaves, and flower parts 
come in four, five, or many whorls. Vascular tissue forms a ring in the stem. 
Eudicots can be herbaceous, or produce woody tissues. Most eudicots 
produce pollen that is trisulcate or triporate, with three furrows or pores. 
The root system is usually anchored by one main root. Eudicots comprise 


two-thirds of all flowering plants. The major differences between monocots 
and eudicots are summarized in [link]. Many species exhibit characteristics 
that belong to either group; as such, the classification of a plant as a 
monocot or a eudicot is not always clearly evident. 


Comparison of Structural Characteristics of Monocots and 


Eudicots 
Characteristic 
Cotyledon 


Veins in 
Leaves 


Stem Vascular 
Tissue 


Roots 


Root Vascular 
Tissues 


Pollen 


Flower Parts 


Monocot 


One 


Parallel 


Scattered 


Network of 
adventitious roots 


Xylem in ring 
pattern 


Single pore or 
furrow 


Multiples of three 


Eudicot 


Two 


Network (branched) 


Arranged in ring pattern 


Tap root with many 
lateral roots 


Xylem in X or star 
pattern 


Three pores or furrows 


Multiples of four or five 
and whorls 


Asexual Reproduction 


Introduction 

" From the sexual, or amatorial, generation of plants new varieties, or 
improvements, are frequently obtained; as many of the young plants from 
seeds are dissimilar to the parent, and some of them superior to the parent in 
the qualities we wish to possess... Sexual reproduction is the chef d'oeuvre, 
the master-piece of nature." Erasmus Darwin, English physician and 
grandfather of Charles Darwin, in Phytologia, (1800) 


Sexual reproduction is certainly one way to produce the next generation, 
but it is not the only way. And in some situations, it might not be the best 
way. Many plants are able to propagate themselves using asexual 
reproduction by simply growing a new individual by mitosis. This method 
does not require the investment required to produce a flower, attract 
pollinators, or find a means of seed dispersal. Asexual reproduction 
produces plants that are genetically identical to the parent plant because no 
mixing of male and female gametes takes place. Traditionally, these plants 
survive well under stable environmental conditions when compared with 
plants produced from sexual reproduction because they carry genes 
identical to those of their parents. 


Many different structures facilitate asexual reproduction ({link]). Garlic and 
gladiolus have an underground stem called a corm. Bulbs, such as a scaly 
bulb in lilies and a tunicate bulb in daffodils, are other common examples. 
A potato is a stem tuber, while parsnip propagates from a taproot. Ginger 
and iris produce rhizomes, while ivy uses an adventitious root (a root 
arising from a plant part other than the main or primary root), and the 
strawberry plant has a stolon, which is also called a runner. In each case, the 
tissue was grown via mitosis and becomes a new individual when separated 
from the 'parent' plant. 


Different types of stems allow 
for asexual reproduction. (a) 
The corm of a garlic plant looks 
similar to (b) a tulip bulb, but 
the corm is solid tissue, while 
the bulb consists of layers of 
modified leaves that surround 
an underground stem. Both 
corms and bulbs can self- 
propagate, giving rise to new 
plants. (c) Ginger forms masses 


of stems called rhizomes that 
can give rise to multiple plants. 
(d) Potato plants form fleshy 
stem tubers. Each eye in the 
stem tuber can give rise toa 
new plant. (e) Strawberry plants 
form stolons: stems that grow at 
the soil surface or just below 
ground and can give rise to new 
plants. (credit a: modification of 
work by Dwight Sipler; credit c: 
modification of work by Albert 
Cahalan, USDA ARS; credit d: 
modification of work by 
Richard North; credit e: 
modification of work by Julie 
Magro) 


Some plants can produce seeds without fertilization. Either the ovule or part 
of the ovary, which is diploid in nature, gives rise to a new seed. This 
method of reproduction is known as apomixis. 


One advantage of asexual reproduction is that the resulting plant will reach 
maturity faster. Since the new plant is arising from an adult plant or plant 
parts, it will also be sturdier than a seedling. Asexual reproduction can take 
place by natural or artificial (assisted by humans) means. 


Natural Methods of Asexual Reproduction 


Natural methods of asexual reproduction include strategies listed above that 
plants have developed to self-propagate. Many plants—like ginger, onion, 
gladioli, and dahlia—continue to grow from buds that are present on the 
surface of the stem. In some plants, such as the sweet potato, adventitious 
roots or runners can give rise to new plants [link]. In Bryophyllum and 
kalanchoe, the leaves have small buds on their margins. When these are 


detached from the plant, they grow into independent plants; or, they may 
start growing into independent plants if the leaf touches the soil. Some 
plants can be propagated through cuttings alone. 


Stolon 
(runner) 


A stolon, or runner, is a stem 
that runs along the ground. At 
the nodes, it forms adventitious 
roots and buds that grow into a 
new plant. 


Artificial Methods of Asexual Reproduction 
These methods are frequently employed to give rise to new, and sometimes 


novel, plants. They include grafting, cutting, layering, and 
micropropagation. 


Grafting 


Grafting has long been used to produce novel varieties of roses, citrus 
species, and other plants. In grafting, two plant species are used; part of the 
stem of the desirable plant is grafted onto a rooted plant called the stock. 
The part that is grafted or attached is called the scion. Both are cut at an 
oblique angle (any angle other than a right angle), placed in close contact 
with each other, and are then held together [link]. Matching up these two 
surfaces as closely as possible is extremely important because these will be 
holding the plant together. The vascular systems of the two plants grow and 
fuse, forming a graft. After a period of time, the scion starts producing 
shoots, and eventually starts bearing flowers and fruits. Grafting is widely 
used in viticulture (grape growing) and the citrus industry. Scions capable 
of producing a particular fruit variety are grafted onto root stock with 
specific resistance to disease. 


Grafting is an artificial method of 
asexual reproduction used to 
produce plants combining 
favorable stem characteristics with 
favorable root characteristics. The 
stem of the plant to be grafted is 


known as the scion, and the root is 
called the stock. 


Cutting 


Plants such as coleus and money plant are propagated through stem 
cuttings, where a portion of the stem containing nodes and internodes is 
placed in moist soil and allowed to root. In some species, stems can start 
producing a root even when placed only in water. For example, leaves of 
the African violet will root if kept in water undisturbed for several weeks. 


Layering 


Layering is a method in which a stem attached to the plant is bent and 
covered with soil. Young stems that can be bent easily without any injury 
are preferred. Jasmine and bougainvillea (paper flower) can be propagated 
this way [link]. In some plants, a modified form of layering known as air 
layering is employed. A portion of the bark or outermost covering of the 
stem is removed and covered with moss, which is then taped. Some 
gardeners also apply rooting hormone. After some time, roots will appear, 
and this portion of the plant can be removed and transplanted into a separate 
pot. 


In layering, a part of the stem is 
buried so that it forms a new plant. 
(credit: modification of work by 
Pearson Scott Foresman, donated 
to the Wikimedia Foundation) 


Micropropagation 


Micropropagation (also called plant tissue culture) is a method of 
propagating a large number of plants from a single plant in a short time 
under laboratory conditions [link]. This method allows propagation of rare, 
endangered species that may be difficult to grow under natural conditions, 
are economically important, or are in demand as disease-free plants. 


Micropropagation is used to 
propagate plants in sterile 
conditions. (credit: Nikhilesh 
Sanyal) 


To start plant tissue culture, a part of the plant such as a stem, leaf, embryo, 
anther, or seed can be used. The plant material is thoroughly sterilized using 
a combination of chemical treatments standardized for that species. Under 
sterile conditions, the plant material is placed on a plant tissue culture 
medium that contains all the minerals, vitamins, and hormones required by 
the plant. The plant part often gives rise to an undifferentiated mass known 
as Callus, from which individual plantlets begin to grow after a period of 
time. These can be separated and are first grown under greenhouse 
conditions before they are moved to field conditions. 


Plant Life Spans 


The length of time from the beginning of development to the death of a 
plant is called its life span. The life cycle, on the other hand, is the sequence 
of stages a plant goes through from seed germination to seed production of 
the mature plant. Some plants, such as annuals, only need a few weeks to 
grow, produce seeds and die. Other plants, such as the bristlecone pine, live 
for thousands of years. Some bristlecone pines have a documented age of 
4,500 years [link]. Even as some parts of a plant, such as regions containing 
meristematic tissue—the area of active plant growth consisting of 
undifferentiated cells capable of cell division—continue to grow, some parts 
undergo programmed cell death (apoptosis). The cork found on stems, and 
the water-conducting tissue of the xylem, for example, are composed of 
dead cells. 


The bristlecone pine, shown here in 
the Ancient Bristlecone Pine Forest in 
the White Mountains of eastern 
California, has been known to live for 
4,500 years. (credit: Rick Goldwaser) 


Plant species that complete their lifecycle in one season are known as 
annuals, an example of which is Arabidopsis, or mouse-ear cress. Biennials 
such as carrots complete their lifecycle in two seasons. In a biennial’s first 


season, the plant has a vegetative phase, whereas in the next season, it 
completes its reproductive phase. Commercial growers harvest the carrot 
roots after the first year of growth, and do not allow the plants to flower. 
Perennials, such as the magnolia, complete their lifecycle in two years or 
more. 


In another classification based on flowering frequency, monocarpic plants 
flower only once in their lifetime; examples include bamboo and yucca. 
During the vegetative period of their life cycle (which may be as long as 
120 years in some bamboo species), these plants may reproduce asexually 
and accumulate a great deal of food material that will be required during 
their once-in-a-lifetime flowering and setting of seed after fertilization. 
Soon after flowering, these plants die. Polycarpic plants form flowers many 
times during their lifetime. Fruit trees, such as apple and orange trees, are 
polycarpic; they flower every year. Other polycarpic species, such as 
perennials, flower several times during their life span, but not each year. By 
this means, the plant does not require all its nutrients to be channeled 
towards flowering each year. 


As is the case with all living organisms, genetics and environmental 
conditions have a role to play in determining how long a plant will live. 
Susceptibility to disease, changing environmental conditions, drought, cold, 
and competition for nutrients are some of the factors that determine the 
survival of a plant. Plants continue to grow, despite the presence of dead 
tissue such as cork. Individual parts of plants, such as flowers and leaves, 
have different rates of survival. In many trees, the older leaves turn yellow 
and eventually fall from the tree. Leaf fall is triggered by factors such as a 
decrease in photosynthetic efficiency, due to shading by upper leaves, or 
oxidative damage incurred as a result of photosynthetic reactions. The 
components of the part to be shed are recycled by the plant for use in other 
processes, such as development of seed and storage. This process is known 
as nutrient recycling. 


The aging of a plant and all the associated processes is known as 
senescence, which is marked by several complex biochemical changes. One 
of the characteristics of senescence is the breakdown of chloroplasts, which 
is characterized by the yellowing of leaves. The chloroplasts contain 


components of photosynthetic machinery such as membranes and proteins. 
Chloroplasts also contain DNA. The proteins, lipids, and nucleic acids are 
broken down by specific enzymes into smaller molecules and salvaged by 
the plant to support the growth of other plant tissues. 


The complex pathways of nutrient recycling within a plant are not well 
understood. Hormones are known to play a role in senescence. Applications 
of cytokinins and ethylene delay or prevent senescence; in contrast, 
abscissic acid causes premature onset of senescence. 


The Plant Body 


Introduction 

" A mile and a half from town, I came to a grove of tall cocoanut trees, with 
clean, branchless stems reaching straight up sixty or seventy feet and 
topped with a spray of green foliage sheltering clusters of cocoanuts—not 
more picturesque than a forest of colossal ragged parasols, with bunches of 
magnified grapes under them, would be. I once heard a grouty northern 
invalid say that a cocoanut tree might be poetical, possibly it was; but it 
looked like a feather-duster struck by lightning. I think that describes it 
better than a picture—and yet, without any question, there is something 
fascinating about a cocoanut tree—and graceful, too." Mark Twain, 
Roughing it, (1913) 

Palm tree on a tropical beach 


Palm tree on a beach, Tulum, Mexico. 
(Photo by David A. Rintoul) 


Twain's observations about the "cocoanut tree" focuses on some of the more 
obvious parts of a plant: the stem, the leaves, the seeds, etc. Some of the 
other parts of a plant are less obvious, but not less important to the health 
and well-being of the organism. Like animals, plants have organelles, cells, 
tissues and organs. 


Plant Organ Systems 


In plants, just as in animals, similar cells working together form a tissue. 
When different types of tissues work together to perform a unique function, 
they form an organ; organs working together form organ systems. Vascular 
plants have two distinct organ systems: a shoot system, and a root system. 
The shoot system consists of two portions: the vegetative (non- 
reproductive) parts of the plant, such as the leaves and the stems, and the 
reproductive parts of the plant, which include flowers and fruits. The shoot 
system generally grows above ground, where it absorbs the light needed for 
photosynthesis. The root system, which supports the plants and absorbs 
water and minerals, is usually underground. [link] shows the organ systems 
of a typical plant. 


Reproductive 


Vegetative 


Shoot system 


Root system 


The shoot system of a plant 
consists of leaves, stems, flowers, 
and fruits. The root system 
anchors the plant while absorbing 
water and minerals from the soil. 


Plant Tissues 


Plants are multicellular eukaryotes with tissue systems made of various cell 
types that carry out specific functions. Plant tissue systems fall into one of 
two general types: meristematic tissue, and permanent (or non- 
meristematic) tissue. Cells of the meristematic tissue are found in 
meristems, which are plant regions of continuous cell division and growth. 
Meristematic tissue cells are either undifferentiated or incompletely 
differentiated, and they continue to divide and contribute to the growth of 
the plant. In contrast, permanent tissue consists of plant cells that are no 
longer actively dividing. 


Meristematic tissues consist of three types, based on their location in the 
plant. Apical meristems contain meristematic tissue located at the tips of 
stems and roots, which enable a plant to extend in length. Lateral 
meristems facilitate growth in thickness or girth in a maturing plant. 
Intercalary meristems occur only in monocots, at the bases of leaf blades 
and at nodes (the areas where leaves attach to a stem). This tissue enables 
the monocot leaf blade to increase in length from the leaf base; for example, 
it allows lawn grass leaves to elongate even after repeated mowing. 


Meristems produce cells that quickly differentiate, or specialize, and 
become permanent tissue. Such cells take on specific roles and lose their 
ability to divide further. They differentiate into three main types: dermal, 
vascular, and ground tissue. Dermal tissue covers and protects the plant, 
and vascular tissue transports water, minerals, and sugars to different parts 
of the plant. Ground tissue serves as a site for photosynthesis, provides a 


supporting matrix for the vascular tissue, and helps to store water and 
sugars. 


Secondary tissues are either simple (composed of similar cell types) or 
complex (composed of different cell types). Dermal tissue, for example, is a 
simple tissue that covers the outer surface of the plant and controls gas 
exchange. Vascular tissue is an example of a complex tissue, and is made of 
two specialized conducting tissues: xylem and phloem. Xylem tissue 
transports water and nutrients from the roots to different parts of the plant, 
and includes three different cell types: vessel elements and tracheids (both 
of which conduct water), and xylem parenchyma. Phloem tissue, which 
transports organic compounds from the site of photosynthesis to other parts 
of the plant, consists of four different cell types: sieve cells (which conduct 
photosynthates), companion cells, phloem parenchyma, and phloem fibers. 
Unlike xylem conducting cells, phloem conducting cells are alive at 
maturity. The xylem and phloem always lie adjacent to each other ({link]). 
In stems, the xylem and the phloem form a structure called a vascular 
bundle; in roots, this is termed the vascular cylinder. 


200 ym 


This light micrograph shows a cross 
section of a squash (Curcurbita maxima) 
stem. Each teardrop-shaped vascular 


bundle consists of large xylem vessels 
toward the inside and smaller phloem 
cells toward the outside. Xylem cells, 
which transport water and nutrients from 
the roots to the rest of the plant, are dead 
at functional maturity. Phloem cells, 
which transport sugars and other organic 
compounds from photosynthetic tissue to 
the rest of the plant, are living. The 
vascular bundles are encased in ground 
tissue and surrounded by dermal tissue. 
(credit: modification of work by " 
(biophotos)"/Flickr; scale-bar data from 
Matt Russell) 


Stems 


Stems are a part of the shoot system of a plant. They may range in length 
from a few millimeters to hundreds of meters, and also vary in diameter, 
depending on the plant type. Stems are usually above ground, although the 
stems of some plants, such as the potato, also grow underground. Stems 
may be herbaceous (soft) or woody in nature. Their main function is to 
provide support to the plant, holding leaves, flowers and buds; in some 
cases, stems also store food for the plant. A stem may be unbranched, like 
that of a palm tree, or it may be highly branched, like that of an oak or pine 
tree. The stem of the plant connects the roots to the leaves, helping to 
transport absorbed water and minerals to different parts of the plant. It also 
helps to transport the products of photosynthesis, namely sugars, from the 
leaves to the rest of the plant. 


Plant stems, whether above or below ground, are characterized by the 
presence of nodes and internodes ([link]). Nodes are points of attachment 
for leaves, aerial roots, and flowers. The stem region between two nodes is 
called an internode. The stalk that extends from the stem to the base of the 
leaf is the petiole. An axillary bud is usually found in the axil—the area 


between the base of a leaf and the stem—where it can give rise to a branch 
or a flower. The apex (tip) of the shoot contains the apical meristem within 
the apical bud. 


Internode 


Petiole 


Leaves are attached to the plant 
stem at areas called nodes. An 
internode is the stem region 
between two nodes. The petiole is 
the stalk connecting the leaf to the 
stem. The leaves just above the 
nodes arose from axillary buds. 


Stem Anatomy 


The stem and other plant organs arise from the ground tissue, and are 
primarily made up of simple tissues formed from three types of cells: 


parenchyma, collenchyma, and sclerenchyma cells. 


Parenchyma cells are the most common plant cells ([link]). They are found 
in the stem, the root, the inside of the leaf, and the pulp of the fruit. 
Parenchyma cells are responsible for metabolic functions, such as 
photosynthesis, and they help repair and heal wounds. Some parenchyma 
cells also store starch. 


The stem of common St John's 
Wort (Hypericum perforatum) is 
shown in cross section in this light 
micrograph. The central pith 
(greenish-blue, in the center) and 
peripheral cortex (narrow zone 3— 
5 cells thick just inside the 
epidermis) are composed of 
parenchyma cells. Vascular tissue 
composed of xylem (red) and 
phloem tissue (green, between the 
xylem and cortex) surrounds the 
pith. (credit: Rolf-Dieter Mueller) 


Collenchyma cells are elongated cells with unevenly thickened walls 
({link]). They provide structural support, mainly to the stem and leaves. 
These cells are alive at maturity and are usually found below the epidermis. 
The “strings” of a celery stalk are an example of collenchyma cells. 


4 


Ge 


i) ( Ss) 
ik 14 @ 
Collenchyma cell walls are uneven 
in thickness, as seen in this light 
micrograph. They provide support 
to plant structures. (credit: 
modification of work by Carl 


Szczerski; scale-bar data from 
Matt Russell) 


Sclerenchyma cells also provide support to the plant, but unlike 
collenchyma cells, many of them are dead at maturity. There are two types 
of sclerenchyma cells: fibers and sclereids. Both types have secondary cell 
walls that are thickened with deposits of lignin, an organic compound that is 
a key component of wood. Fibers are long, slender cells; sclereids are 
smaller-sized. Sclereids give pears their gritty texture. Humans use 
sclerenchyma fibers to make linen and rope ([link]). 


Phloem 


Epidermis Cortex Sclerenchyma 
(a) 


The central pith and outer cortex of the (a) flax 
stem are made up of parenchyma cells. Inside the 
cortex is a layer of sclerenchyma cells, which 
make up the fibers in flax rope and clothing. 
Humans have grown and harvested flax for 
thousands of years. In (b) this drawing, fourteenth- 
century women prepare linen. The (c) flax plant is 
grown and harvested for its fibers, which are used 
to weave linen, and for its seeds, which are the 
source of linseed oil. (credit a: modification of 
work by Emmanuel Boutet based on original work 
by Ryan R. MacKenzie; credit c: modification of 
work by Brian Dearth; scale-bar data from Matt 
Russell) 


Like the rest of the plant, the stem has three tissue systems: dermal, 
vascular, and ground tissue. Each is distinguished by characteristic cell 
types that perform specific tasks necessary for the plant’s growth and 
survival. 


Dermal Tissue 


The dermal tissue of the stem consists primarily of epidermis, a single layer 
of cells covering and protecting the underlying tissue. Woody plants have a 
tough, waterproof outer layer of cork cells commonly known as bark, which 
further protects the plant from damage. Epidermal cells are the most 
numerous and least differentiated of the cells in the epidermis. The 
epidermis of a leaf also contains openings known as stomata, through which 
the exchange of gases takes place ([{link]). Two cells, known as guard cells, 
surround each leaf stoma, controlling its opening and closing and thus 
regulating the uptake of carbon dioxide and the release of oxygen and water 
vapor. Trichomes are hair-like structures on the epidermal surface. They 
help to reduce transpiration (the loss of water by aboveground plant parts), 
increase solar reflectance, and store compounds that defend the leaves 
against predation by herbivores. 


Guard cells Open stoma Closed stoma 
(b) 


L> Guard cells 


Stomatal pore 


= Epidermal cells 


Openings called stomata (singular: stoma) allow a plant to take 
up carbon dioxide and release oxygen and water vapor. The (a) 
colorized scanning-electron micrograph shows a closed stoma 
of a eudicot. Each stoma is flanked by two guard cells that 
regulate its (b) opening and closing. The (c) guard cells sit 
within the layer of epidermal cells (credit a: modification of 
work by Louisa Howard, Rippel Electron Microscope Facility, 
Dartmouth College; credit b: modification of work by June 
Kwak, University of Maryland; scale-bar data from Matt 
Russell) 


Vascular Tissue 


The xylem and phloem that make up the vascular tissue of the stem are 
arranged in distinct strands called vascular bundles, which run up and down 
the length of the stem. When the stem is viewed in cross section, the 
vascular bundles of eudicot stems are arranged in a ring. In plants with 
stems that live for more than one year, the individual bundles grow together 
and produce the characteristic growth rings. In monocot stems, the vascular 
bundles are randomly scattered throughout the ground tissue ([Link]). 


Eudicot stem Monocot stem 


In (a) eudicot stems, vascular bundles are arranged 
around the periphery of the ground tissue. The 
xylem tissue is located toward the interior of the 
vascular bundle, and phloem is located toward the 
exterior. Sclerenchyma fibers cap the vascular 
bundles. In (b) monocot stems, vascular bundles 
composed of xylem and phloem tissues are 
scattered throughout the ground tissue. 


Xylem tissue has three types of cells: xylem parenchyma, tracheids, and 
vessel elements. The latter two types conduct water and are dead at 
maturity. Tracheids are xylem cells with thick secondary cell walls that are 
lignified. Water moves from one tracheid to another through regions on the 
side walls known as pits, where secondary walls are absent. Vessel elements 
are xylem cells with thinner walls; they are shorter than tracheids. Each 
vessel element is connected to the next by means of a perforation plate at 
the end walls of the element. Water moves through the perforation plates to 
travel up the plant. 


Phloem tissue is composed of sieve-tube cells, companion cells, phloem 
parenchyma, and phloem fibers. A series of sieve-tube cells (also called 
sieve-tube elements) are arranged end to end to make up a long sieve tube, 
which transports organic substances such as sugars and amino acids. The 
sugars flow from one sieve-tube cell to the next through perforated sieve 
plates, which are found at the end junctions between two cells. Although 
still alive at maturity, the nucleus and other cell components of the sieve- 
tube cells have disintegrated. Companion cells are found alongside the 
sieve-tube cells, providing them with metabolic support. The companion 
cells contain more ribosomes and mitochondria than the sieve-tube cells, 
which lack some cellular organelles. 


Ground Tissue 


Ground tissue is mostly made up of parenchyma cells, but may also contain 
collenchyma and sclerenchyma cells that help support the stem. The ground 
tissue towards the interior of the vascular tissue in a stem or root is known 
as pith, while the layer of tissue between the vascular tissue and the 
epidermis is known as the cortex. 


Growth in Stems 


Growth in plants occurs as the stems and roots lengthen. Some plants, 
especially those that are woody, also increase in thickness during their life 
span. The increase in length of the shoot and the root is referred to as 
primary growth, and is the result of cell division in the shoot apical 
meristem. Secondary growth is characterized by an increase in thickness 
or girth of the plant, and is caused by cell division in the lateral meristem. 
[link] shows the areas of primary and secondary growth in a plant. 
Herbaceous plants mostly undergo primary growth, with hardly any 
secondary growth or increase in thickness. Secondary growth or “wood” is 
noticeable in woody plants; it occurs in some eudicots, but occurs very 
rarely in monocots. 


Primary growth Secondary growth 


Primary 
Secondary Cork 
phloem phloem 


Pith 


~ / Cortex 


Vascular 
cambium 


Phloem Sclerenchyma 


F Epidermis 
Xylem Primary 


xylem Cork 


Secondary cambium 
xylem 


In woody plants, primary growth is followed by 
secondary growth, which allows the plant stem to 
increase in thickness or girth. Secondary vascular 

tissue is added as the plant grows, as well as a cork 
layer. The bark of a tree extends from the vascular 
cambium to the epidermis. 


Some plant parts, such as stems and roots, continue to grow throughout a 
plant’s life: a phenomenon called indeterminate growth. Other plant parts, 
such as leaves and flowers, exhibit determinate growth, which ceases when 
a plant part reaches a particular size. 


Annual Rings 


The activity of the vascular cambium gives rise to annual growth rings. 
During the spring growing season, cells of the secondary xylem have a 
large internal diameter and their primary cell walls are not extensively 
thickened. This is known as early wood, or spring wood. During the fall 


season, the secondary xylem develops thickened cell walls, forming late 
wood, or autumn wood, which is denser than early wood. This alternation 
of early and late wood is due largely to a seasonal decrease in the number of 
vessel elements and a seasonal increase in the number of tracheids. It results 
in the formation of an annual ring, which can be seen as a circular ring in 
the cross section of the stem ({link]). An examination of the number of 
annual rings and their nature (such as their size and cell wall thickness) can 
reveal the age of the tree and the prevailing climatic conditions during each 
season. 


The rate of wood growth increases 

in summer and decreases in winter, 

producing a characteristic ring for 

each year of growth. Seasonal 
changes in weather patterns can 
also affect the growth rate—note 
how the rings vary in thickness. 
(credit: Adrian Pingstone) 


Roots 


The roots of seed plants have three major functions: anchoring the plant to 
the soil, absorbing water and minerals and transporting them upwards, and 
storing the products of photosynthesis. Some roots are modified to absorb 
moisture and exchange gases. Most roots are underground. Some plants, 
however, also have adventitious roots, which emerge above the ground 
from the shoot. 


Types of Root Systems 


Root systems are mainly of two types ([link]). Eudicots have a tap root 
system, while monocots have a fibrous root system. A tap root system has 
a main root that grows down vertically, and from which many smaller 
lateral roots arise. Dandelions are a good example; their tap roots usually 
break off when trying to pull these weeds, and they can regrow another 
shoot from the remaining root). A tap root system penetrates deep into the 
soil. In contrast, a fibrous root system is located closer to the soil surface, 
and forms a dense network of roots that also helps prevent soil erosion 
(lawn grasses are a good example, as are wheat, rice, and corn). Some 
plants have a combination of tap roots and fibrous roots. Plants that grow in 
dry areas often have deep root systems, whereas plants growing in areas 
with abundant water are likely to have shallower root systems. 


(a) Taproot system (b) Fibrous root system 


(a) Tap root systems have a main root that 
grows down, while (b) fibrous root systems 
consist of many small roots. (credit b: 
modification of work by “Austen 
Squarepants”/Flickr) 


Leaves 


Leaves are the main sites for photosynthesis: the process by which plants 
synthesize food. Most leaves are usually green, due to the presence of 
chlorophyll in the leaf cells. However, some leaves may have different 
colors, caused by other plant pigments that mask the green chlorophyll. 


The thickness, shape, and size of leaves are adapted to the environment. 
Each variation helps a plant species maximize its chances of survival in a 
particular habitat. Usually, the leaves of plants growing in tropical 
rainforests have larger surface areas than those of plants growing in deserts 
or very cold conditions, which are likely to have a smaller surface area to 
minimize water loss. 


Structure of a Typical Leaf 


Each leaf typically has a leaf blade called the lamina, which is also the 
widest part of the leaf. Some leaves are attached to the plant stem by a 
petiole. Leaves that do not have a petiole and are directly attached to the 
plant stem are called sessile leaves. Small green appendages usually found 
at the base of the petiole are known as stipules. Most leaves have a midrib, 
which travels the length of the leaf and branches to each side to produce 
veins of vascular tissue. The edge of the leaf is called the margin. [link] 
shows the structure of a typical eudicot leaf. 


Deceptively simple in appearance, 
a leaf is a highly efficient 
structure. 


Within each leaf, the vascular tissue forms veins. The arrangement of veins 
in a leaf is called the venation pattern. Monocots and eudicots differ in their 
patterns of venation ({link]). Monocots have parallel venation; the veins run 


in straight lines across the length of the leaf without converging at a point. 
In eudicots, however, the veins of the leaf have a net-like appearance, 
forming a pattern known as reticulate venation. One extant plant, the 
Ginkgo biloba, has dichotomous venation where the veins fork. 


(a) (b) (c) 


(a) Tulip (Tulipa), a monocot, has leaves with 
parallel venation. The netlike venation in this (b) 
linden (Tilia cordata) leaf distinguishes it as a 
eudicot. The (c) Ginkgo biloba tree has dichotomous 
venation. (credit a photo: modification of work by 
“Drewboy64”/Wikimedia Commons; credit b photo: 
modification of work by Roger Griffith; credit c 
photo: modification of work by 
"geishaboy500"/Flickr; credit abc illustrations: 
modification of work by Agnieszka Kwiecien) 


Plant Sensory Systems and Responses 


Introduction 

"Plants are extraordinary. For instance ... if you pinch a leaf of a plant you 
set off electrical impulse. You can't touch a plant without setting off an 
electrical impulse ... There is no question that plants have all kinds of 
sensitivities. They do a lot of responding to an environment. They can do 
almost anything you can think of. " Barbara McClintock, Nobel prize- 
winning geneticist, in George Ritzer and Barry Smart, Handbook of Social 
Theory (2001) 


Animals can respond to environmental factors by moving to a new location. 
Plants, however, are rooted in place and must respond to the surrounding 
environmental factors. Plants have sophisticated systems to detect and 
respond to light, gravity, temperature, and physical touch. Receptors sense 
environmental factors and relay the information to effector systems—often 
through intermediate chemical messengers—to bring about plant responses. 


Plant Responses to Light 


Plants have a number of sophisticated uses for light that go far beyond their 
ability to photosynthesize low-molecular-weight sugars using only carbon 
dioxide, light, and water. Photomorphogenesis is the growth and 
development of plants in response to light. It allows plants to optimize their 
use of light and space. Photoperiodism is the ability to use light to track 
time. Plants can tell the time of day and time of year by sensing and using 
various wavelengths of sunlight. Phototropism is a directional response 
that allows plants to grow towards, or even away from, light. 


The sensing of light in the environment is important to plants; it can be 
crucial for competition and survival. The response of plants to light is 
mediated by different photoreceptors, which are comprised of a protein 
covalently bonded to a light-absorbing pigment called a chromophore. 
Together, the two are called a chromoprotein. 


Phototropism 


Phototropism—the directional bending of a plant toward or away from a 
light source—is a response to blue wavelengths of light. Positive 
phototropism is growth towards a light source ({link]), while negative 
phototropism is growth away from light. 


In their 1880 treatise The Power of Movements in Plants, Charles Darwin 
and his son Francis first described phototropism as the bending of seedlings 
toward light. Darwin observed that light was perceived by the tip of the 
plant (the apical meristem), but that the response (bending) took place in a 
different part of the plant. They concluded that the signal had to travel from 
the apical meristem to the base of the plant. 


Sunflowers in a field near Hutchinson, KS display a 
phototropic response by bending toward the light. 
(credit: David A. Rintoul) 


In 1913, Peter Boysen-Jensen demonstrated that a chemical signal produced 
in the plant tip was responsible for the bending at the base. He cut off the 
tip of a seedling, covered the cut section with a layer of gelatin, and then 
replaced the tip. The seedling bent toward the light when illuminated. 
However, when impermeable mica flakes were inserted between the tip and 
the cut base, the seedling did not bend. A refinement of the experiment 
showed that the signal traveled on the shaded side of the seedling. When the 


mica plate was inserted on the illuminated side, the plant did bend towards 
the light. Therefore, the chemical signal was a growth stimulant because the 
phototropic response involved faster cell elongation on the shaded side than 
on the illuminated side. We now know that the plant hormone auxin 
influences plant stem cell elongation, and accumulates on the shaded side of 
stems. 


Plant Responses to Gravity 


Whether or not they germinate in the light or in total darkness, shoots 
usually sprout up from the ground, and roots grow downward into the 
ground. A plant laid on its side in the dark will send shoots upward when 
given enough time. Gravitropism ensures that roots grow into the soil and 
that shoots grow toward sunlight. Growth of the shoot apical tip upward is 
called negative gravitropism, whereas growth of the roots downward is 
called positive gravitropism. 


Amyloplasts (also known as statoliths) are specialized plastids that contain 
starch granules and settle downward in response to gravity. Amyloplasts are 
found in shoots and in specialized cells of the root cap. When a plant is 
tilted, the statoliths drop to the new bottom cell wall. A few hours later, the 
shoot or root will show growth in the new vertical direction. 


The mechanism that mediates gravitropism is reasonably well understood. 
When amyloplasts settle to the bottom of the gravity-sensing cells in the 
root or shoot, they physically contact the endoplasmic reticulum (ER), 
causing the release of calcium ions from inside the ER. This calcium 
signaling in the cells causes polar transport of the plant hormone auxin to 
the bottom of the cell. In roots, a high concentration of auxin inhibits cell 
elongation. The effect slows growth on the lower side of the root, while 
cells develop normally on the upper side. Auxin has the opposite effect in 
shoots, where a higher concentration at the lower side of the shoot 
stimulates cell expansion, causing the shoot to grow up. After the shoot or 
root begin to grow vertically, the amyloplasts return to their normal 
position. Other hypotheses—involving the entire cell in the gravitropism 
effect—have been proposed to explain why some mutants that lack 
amyloplasts may still exhibit a weak gravitropic response. 


Growth Responses 


A plant’s sensory response to external stimuli relies on chemical 
messengers (hormones). Plant hormones affect all aspects of plant life, from 
flowering to fruit setting and maturation, and from phototropism to leaf fall. 
Potentially every cell in a plant can produce plant hormones. They can act 
in their cell of origin or be transported to other portions of the plant body, 
with many plant responses involving the synergistic or antagonistic 
interaction of two or more hormones. In contrast, animal hormones are 
produced in specific glands and transported to a distant site for action, and 
they act alone. 


Plant hormones are a group of unrelated chemical substances that affect 
plant morphogenesis. Five major plant hormones are traditionally 
described: auxins, cytokinins, gibberellins, ethylene, and abscisic acid. In 
addition, other nutrients and environmental conditions can be characterized 
as growth factors. 


Auxins 


The term auxin is derived from the Greek word auxein, which means "to 
grow.” Auxins are the main hormones responsible for cell elongation in 
phototropism and gravitropism. They also control the differentiation of 
meristem into vascular tissue, and promote leaf development and 
arrangement. While many synthetic auxins are used as herbicides, IAA (a 
type of auxin) is the only naturally occurring auxin that shows physiological 
activity. Apical dominance—the inhibition of lateral bud formation—is 
triggered by auxins produced in the apical meristem. Flowering, fruit 
setting and ripening, and inhibition of abscission (leaf falling) are other 
plant responses under the direct or indirect control of auxins. Auxins also 
act as a relay for the effects of the blue light and red/far-red responses. 


Commercial use of auxins is widespread in plant nurseries and for crop 
production. IAA is used as a rooting hormone to promote growth of 
adventitious roots on cuttings and detached leaves. Applying synthetic 
auxins to tomato plants in greenhouses promotes normal fruit development. 


Outdoor application of auxin promotes synchronization of fruit setting and 
dropping to coordinate the harvesting season. Fruits such as seedless 
cucumbers can be induced to set fruit by treating unfertilized plant flowers 
with auxins. 


Cytokinins 


The effect of cytokinins was first reported when it was found that adding 
the liquid endosperm of coconuts to developing plant embryos in culture 
stimulated their growth. The stimulating growth factor was found to be 
cytokinin, a hormone that promotes cytokinesis (cell division). Almost 200 
naturally occurring or synthetic cytokinins are known to date. Cytokinins 
are most abundant in growing tissues, such as roots, embryos, and fruits, 
where cell division is occurring. Cytokinins are known to delay senescence 
in leaf tissues, promote mitosis, and stimulate differentiation of the 
meristem in shoots and roots. Many effects on plant development are under 
the influence of cytokinins, either in conjunction with auxin or another 
hormone. For example, apical dominance seems to result from a balance 
between auxins that inhibit lateral buds, and cytokinins that promote 
bushier growth. 


Gibberellins 


Gibberellins (GAs) are a group of about 125 closely related plant 
hormones that stimulate shoot elongation, seed germination, and fruit and 
flower maturation. GAs are synthesized in the root and stem apical 
meristems, young leaves, and seed embryos. In urban areas, GA antagonists 
are sometimes applied to trees under power lines to control growth and 
reduce the frequency of pruning. 


GAs break dormancy (a state of inhibited growth and development) in the 
seeds of plants that require exposure to cold or light to germinate. Abscisic 
acid is a strong antagonist of GA action. Other effects of GAs include 
gender expression, seedless fruit development, and the delay of senescence 


in leaves and fruit. Seedless grapes are obtained through standard breeding 
methods and contain inconspicuous seeds that fail to develop. Because GAs 
are produced by the seeds, and because fruit development and stem 
elongation are under GA control, these varieties of grapes would normally 
produce small fruit in compact clusters. Maturing grapes are routinely 
treated with GA to promote larger fruit size, as well as looser bunches 
(longer stems), which reduces the instance of mildew infection ([Link]). 


In grapes, application of 
gibberellic acid increases 
the size of fruit and 


loosens clustering. 
(credit: Bob Nichols, 
USDA) 


Abscisic Acid 


The plant hormone abscisic acid (ABA) was first discovered as the agent 
that causes the abscission or dropping of cotton bolls. However, more recent 
studies indicate that ABA plays only a minor role in the abscission process. 
ABA accumulates as a response to stressful environmental conditions, such 
as dehydration, cold temperatures, or shortened day lengths. Its activity 
counters many of the growth-promoting effects of GAs and auxins. ABA 
inhibits stem elongation and induces dormancy in lateral buds. 


ABA induces dormancy in seeds by blocking germination and promoting 
the synthesis of storage proteins. Plants adapted to temperate climates 
require a long period of cold temperature before seeds germinate. This 
mechanism protects young plants from sprouting too early during 
unseasonably warm weather in winter. As the hormone gradually breaks 
down over winter, the seed is released from dormancy and germinates when 
conditions are favorable in spring. Another effect of ABA is to promote the 
development of winter buds; it mediates the conversion of the apical 
meristem into a dormant bud. Low soil moisture causes an increase in 
ABA, which causes stomata to close, reducing water loss in winter buds. 


Ethylene 


Ethylene is associated with fruit ripening, flower wilting, and leaf fall. 
Ethylene is unusual because it is a volatile gas (C)H,). Hundreds of years 
ago, when gas street lamps were installed in city streets, trees that grew 
close to lamp posts developed twisted, thickened trunks and shed their 
leaves earlier than expected. These effects were caused by ethylene 
volatilizing from the lamps. 


Aging tissues (especially senescing leaves) and nodes of stems produce 
ethylene. The best-known effect of the hormone, however, is the promotion 
of fruit ripening. Ethylene stimulates the conversion of starch and acids to 
sugars. Some people store unripe fruit, such as avocadoes, in a sealed paper 
bag to accelerate ripening; the gas released by the first fruit to mature will 
speed up the maturation of the remaining fruit. Ethylene also triggers leaf 


and fruit abscission, flower fading and dropping, and promotes germination 
in some cereals and sprouting of bulbs and potatoes. 


Ethylene is widely used in agriculture. Commercial fruit growers control 
the timing of fruit ripening with application of the gas. Horticulturalists 
inhibit leaf dropping in ornamental plants by removing ethylene from 
greenhouses using fans and ventilation. 


Plant Responses to Wind and Touch 


The shoot of a pea plant winds around a trellis, while a tree grows on an 
angle in response to strong prevailing winds. These are examples of how 
plants respond to touch or wind. 


The movement of a plant subjected to constant directional pressure is called 
thigmotropism, from the Greek words thigma meaning “touch,” and 
tropism implying “direction.” Tendrils are one example of this. The 
meristematic region of tendrils is very touch sensitive; light touch will 
evoke a quick coiling response. Cells in contact with a support surface 
contract, whereas cells on the opposite side of the support expand. 
Application of jasmonic acid is sufficient to trigger tendril coiling without a 
mechanical stimulus. 


A thigmonastic response is a touch response independent of the direction of 
stimulus. In the Venus flytrap, two modified leaves are joined at a hinge and 
lined with thin fork-like tines along the outer edges. Tiny hairs are located 
inside the trap. When an insect brushes against these trigger hairs, touching 
two or more of them in succession, the leaves close quickly, trapping the 
prey. Glands on the leaf surface secrete enzymes that slowly digest the 
insect. The released nutrients are absorbed by the leaves, which reopen for 
the next meal. 


Thigmomorphogenesis is a slow developmental change in the shape of a 
plant subjected to continuous mechanical stress. When trees bend in the 
wind, for example, growth is usually stunted and the trunk thickens. 
Strengthening tissue, especially xylem, is produced to add stiffness to resist 
the wind’s force. Researchers hypothesize that mechanical strain induces 


growth and differentiation to strengthen the tissues. Ethylene and jasmonate 
are likely involved in thigmomorphogenesis. 


Reproductive Development and Structure 


Introduction 
"Flowers are the sweetest things that God ever made, and forgot to put a 
soul into." Henry Ward Beecher, in Proverbs from Plymouth Pulpit (1887) 


Flowers have fascinated humans for millenia, with their marvelous shapes 
and enticing aromas. But the plant has another goal in mind besides 
pleasing the human eye and nose, and that is reproduction. Sexual 
reproduction takes place with slight variations in different groups of plants. 
Plants have two distinct stages in their lifecycle: the gametophyte stage and 
the sporophyte stage. The haploid gametophyte produces the male and 
female gametes by mitosis in distinct multicellular structures. Fusion of the 
male and females gametes forms the diploid zygote, which develops into 
the sporophyte. After reaching maturity, the diploid sporophyte produces 
spores by meiosis, which in turn divide by mitosis to produce the haploid 
gametophyte. The new gametophyte produces gametes, and the cycle 
continues. This is the alternation of generations, and is typical of plant 
reproduction ([link]). 


Angiosperm Life Cycle 


Flower 


Zygote within 
parent ovary a 
Independent 
Sporophyte 
Embryo within Mitosis 


ee 


Mitosis 


Diploid (2N) 


The angiosperm life cycle with alternation of generations is depicted in 
this diagram. Work by Robert A. Bear and Eva Horne 


The life cycle of higher plants is dominated by the sporophyte stage, with 
the gametophyte borne on the sporophyte. In ferns, the gametophyte is free- 
living and very distinct in structure from the diploid sporophyte. In 
bryophytes, such as mosses, the haploid gametophyte is more developed 
than the sporophyte. 


During the vegetative phase of growth, plants increase in size and produce a 
shoot system and a root system. As they enter the reproductive phase, some 
of the branches start to bear flowers. Many flowers are borne singly, 


whereas some are borne in clusters. The flower is borne on a stalk known as 
a receptacle. Flower shape, color, and size are unique to each species, and 
are often used by taxonomists to classify plants. 


Sexual Reproduction in Angiosperms 


The lifecycle of angiosperms follows the alternation of generations 
explained previously. The haploid gametophyte alternates with the diploid 
sporophyte during the sexual reproduction process of angiosperms. Flowers 
contain the plant’s reproductive structures. 


Flower Structure 


A typical flower has four main parts—or whorls—known as the calyx, 
corolla, androecium, and gynoecium ([link]). The outermost whorl of the 
flower has green, leafy structures known as sepals. The sepals, collectively 
called the calyx, help to protect the unopened bud. The second whorl is 
comprised of petals—usually, brightly colored—collectively called the 
corolla. The number of sepals and petals varies depending on whether the 
plant is a monocot or eudicot. In monocots, petals usually number three or 
multiples of three; in eudicots, the number of petals is four or five, or 
multiples of four and five. Together, the calyx and corolla are known as the 
perianth. The third whorl contains the male reproductive structures and is 
known as the androecium. The androecium has stamens with anthers that 
contain the microsporangia. The innermost group of structures in the flower 
is the gynoecium, or the female reproductive component(s). The carpel is 
the individual unit of the gynoecium and has a stigma, style, and ovary. A 
flower may have one or multiple carpels. 


Stamens 


Petal 


Flower 
Corolla (composed of petals) 
Calyx (composed of sepals) 


The four main parts of the flower are the calyx, corolla, androecium, 
and gynoecium. The androecium is the sum of all the male 
reproductive organs, and the gynoecium is the sum of the female 
reproductive organs. (credit: modification of work by Mariana Ruiz 
Villareal) 


If the anther is missing, what type of reproductive structure will the flower 
be unable to produce? What term is used to describe an incomplete flower 
lacking the androecium? What term describes an incomplete flower lacking 
a gynoecium? 


If all four whorls (the calyx, corolla, androecium, and gynoecium) are 
present, the flower is described as complete. If any of the four parts is 
missing, the flower is known as incomplete. Flowers that contain both an 


androecium and a gynoecium are called perfect, androgynous or 
hermaphrodites. There are two types of incomplete flowers: staminate 
flowers contain only an androecium, and carpellate flowers have only a 
gynoecium ([link]). 


Staminate Carpellate 
flowers flowers 


Stem Corn Silk Ovary 
and root kernels —_ (stigma) 


The corn plant has both staminate 
(male) and carpellate (female) 
flowers. Staminate flowers, which 
are clustered in the tassel at the tip 
of the stem, produce pollen grains. 
Carpellate flower are clustered in 
the immature ears. Each strand of 
silk is a stigma. The corn kernels 
are seeds that develop on the ear 


after fertilization. Also shown is 
the lower stem and root. 


If both male and female flowers are borne on the same plant, the species is 
called monoecious (meaning “one home”): examples are corn and pea. 
Species with male and female flowers borne on separate plants are termed 
dioecious, or “two homes,” examples of which are C. papaya and 
Cannabis. The ovary, which may contain one or multiple ovules, may be 
placed above other flower parts, which is referred to as superior; or, it may 
be placed below the other flower parts, referred to as inferior ((link]). 


Sepals 


Ovaries 


(a) Superior flower (b) Inferior flower 


The (a) lily is a superior flower, which has the ovary 
above the other flower parts. (b) Fuchsia is an inferior 
flower, which has the ovary beneath other flower parts. 

(credit a photo: modification of work by Benjamin 
Zwittnig; credit b photo: modification of work by 
"Koshy Koshy"/Flickr) 


Male Gametophyte (The Pollen Grain) 


The male gametophyte develops and reaches maturity in an immature 
anther. In a plant’s male reproductive organs, development of pollen takes 
place in a structure known as the microsporangium ([link]). The 
microsporangia, which are usually bi-lobed, are pollen sacs in which the 
microspores develop into pollen grains. These are found in the anther, 
which is at the end of the stamen—the long filament that supports the 
anther. 


Se Vicrospore 
} mother cells 


Tapetum 


Pollensacs —~ 
(microsporangia) 


Shown is (a) a cross section of an anther at two 
developmental stages. The immature anther 
(top) contains four microsporangia, or pollen 
sacs. Each microsporangium contains hundreds 
of microspore mother cells that will each give 
rise to four pollen grains. The tapetum supports 
the development and maturation of the pollen 
grains. Upon maturation of the pollen 
(bottom), the pollen sac walls split open and 
the pollen grains (male gametophytes) are 
released. (b) In these scanning electron 
micrographs, pollen sacs are ready to burst, 
releasing their grains. (credit b: modification of 


work by Robert R. Wise; scale-bar data from 
Matt Russell) 


Within the microsporangium, the microspore mother cell divides by meiosis 
to give rise to four microspores, each of which will ultimately form a pollen 
grain ([link]). An inner layer of cells, known as the tapetum, provides 
nutrition to the developing microspores and contributes key components to 
the pollen wall. Mature pollen grains contain two cells: a generative cell 
and a pollen tube cell. The generative cell is contained within the larger 
pollen tube cell. Upon germination, the tube cell forms the pollen tube 
through which the generative cell migrates to enter the ovary. During its 
transit inside the pollen tube, the generative cell divides to form two male 
gametes (sperm cells). Upon maturity, the microsporangia burst, releasing 
the pollen grains from the anther. 


Microspore 
mother cell 


Pollen 
tube cell 


Mature 
pollen 
grains 


nucleus 


Pollen develops from the microspore 
mother cells. The mature pollen grain is 
composed of two cells: the pollen tube 
cell and the generative cell, which is 
inside the tube cell. The pollen grain has 
two coverings: an inner layer (intine) and 
an outer layer (exine). The inset scanning 
electron micrograph shows Arabidopsis 
lyrata pollen grains. (credit “pollen 
micrograph”: modification of work by 
Robert R. Wise; scale-bar data from Matt 
Russell) 


Each pollen grain has two coverings: the exine (thicker, outer layer) and the 
intine ({link]). The exine contains sporopollenin, a complex waterproofing 
substance supplied by the tapetal cells. Sporopollenin allows the pollen to 
survive under unfavorable conditions and to be carried by wind, water, or 
biological agents without undergoing damage. 


Female Gametophyte (The Embryo Sac) 


While the details may vary between species, the overall development of the 
female gametophyte has two distinct phases. First, in the process of 
megasporogenesis, a single cell in the diploid megasporangium—an area of 
tissue in the ovules—undergoes meiosis to produce four megaspores, only 
one of which survives. During the second phase, megagametogenesis, the 
surviving haploid megaspore undergoes mitosis to produce an eight- 
nucleate, seven-cell female gametophyte, also known as the 
megagametophyte or embryo sac. Two of the nuclei—the polar nuclei— 
move to the equator and fuse, forming a single, diploid central cell. This 
central cell later fuses with a sperm to form the triploid endosperm. Three 
nuclei position themselves on the end of the embryo sac opposite the 
micropyle and develop into the antipodal cells, which later degenerate. The 
nucleus closest to the micropyle becomes the female gamete, or egg cell, 
and the two adjacent nuclei develop into synergid cells ({link]). The 
synergids help guide the pollen tube for successful fertilization, after which 
they disintegrate. Once fertilization is complete, the resulting diploid zygote 
develops into the embryo, and the fertilized ovule forms the other tissues of 
the seed. 


A double-layered integument protects the megasporangium and, later, the 
embryo sac. The integument will develop into the seed coat after 
fertilization and protect the entire seed. The ovule wall will become part of 
the fruit. The integuments, while protecting the megasporangium, do not 
enclose it completely, but leave an opening called the micropyle. The 


micropyle allows the pollen tube to enter the female gametophyte for 
fertilization. 


Embryo Sac 


Chalazal end 


Antipodals 


Polar nuclei 


Synergids 


Central Egg cell 


cell 


Micropylar end 


As shown in this diagram of 
the embryo sac in 
angiosperms, the ovule is 
covered by integuments and 
has an opening called a 
micropyle. Inside the 
embryo sac are three 
antipodal cells, two 
synergids, a central cell, and 
the egg cell. 


Pollination and Fertilization 


Introduction 

"Nature is full of by-ends. A moth feeds on a petal, in a moment the pollen 
caught on its breast will be wedding this blossom to another in the next 
county." George Iles, in Canadian Stories (1918) 


In angiosperms, pollination is defined as the placement or transfer of 
pollen from the anther to the stigma of the same flower or another flower. In 
gymnosperms, pollination involves pollen transfer from the male cone to 
the female cone. Upon transfer, the pollen germinates to form the pollen 
tube and the sperm for fertilizing the egg. Pollination has been well studied 
since the time of Gregor Mendel. Mendel successfully carried out self- as 
well as cross-pollination in garden peas while studying how characteristics 
were passed on from one generation to the next. Today’s crops are a result 
of plant breeding, which employs artificial selection to produce the present- 
day cultivars. A case in point is today's corn, which is a result of years of 
breeding that started with its ancestor, teosinte. The teosinte that the ancient 
Mayans originally began cultivating had tiny seeds—vastly different from 
today’s relatively giant ears of corn. Interestingly, though these two plants 
appear to be entirely different, the genetic difference between them is 
miniscule. 


Pollination takes two forms: self-pollination and cross-pollination. Self- 
pollination occurs when the pollen from the anther is deposited on the 
stigma of the same flower, or another flower on the same plant. Cross- 
pollination is the transfer of pollen from the anther of one flower to the 
stigma of another flower on a different individual of the same species. Self- 
pollination occurs in flowers where the stamen and carpel mature at the 
same time, and are positioned so that the pollen can land on the flower’s 
stigma. This method of pollination does not require an investment from the 
plant to provide nectar and pollen as food for pollinators. 


Living species are adapted to ensure survival of their progeny; those that 
fail become extinct. Genetic diversity is therefore required so that in 
changing environmental or stress conditions, some of the progeny can 
survive. Self-pollination leads to the production of plants with less genetic 
diversity, since genetic material from the same plant is used to form both 


gametes, and eventually, the zygote. In contrast, cross-pollination—or out- 
crossing—leads to greater genetic diversity because the microgametophyte 
and megagametophyte are derived from different plants. 


Because cross-pollination allows for more genetic diversity, plants have 
developed many ways to avoid self-pollination. In some species, the pollen 
and the ovary mature at different times. These flowers make self-pollination 
nearly impossible. By the time pollen matures and has been shed, the 
stigma of this flower is mature and can only be pollinated by pollen from 
another flower. Some flowers have developed physical features that prevent 
self-pollination. The primrose is one such flower. Primroses have evolved 
two flower types with differences in anther and stigma length: the pin-eyed 
flower has anthers positioned at the pollen tube’s halfway point, and the 
thrum-eyed flower’s stigma is likewise located at the halfway point. Insects 
easily cross-pollinate while seeking the nectar at the bottom of the pollen 
tube. This phenomenon is also known as heterostyly. Many plants, such as 
cucumber, have male and female flowers located on different parts of the 
plant, thus making self-pollination difficult. In yet other species, the male 
and female flowers are borne on different plants (dioecious). All of these 
are barriers to self-pollination; therefore, the plants depend on pollinators to 
transfer pollen. The majority of pollinators are biotic agents such as insects 
(like bees, flies, and butterflies), bats, birds, and other animals. Other plant 
species are pollinated by abiotic agents, such as wind and water. 


Pollination by Insects 


Bees are perhaps the most important pollinator of many garden plants and 
most commercial fruit trees ((link]). The most common species of bees are 
bumblebees and honeybees. Since bees cannot see the color red, bee- 
pollinated flowers usually have shades of blue, yellow, or other colors. Bees 
collect energy-rich pollen or nectar for their survival and energy needs. 
They visit flowers that are open during the day, are brightly colored, have a 
strong aroma or scent, and have a tubular shape, typically with the presence 
of a nectar guide. A nectar guide includes regions on the flower petals that 
are visible only to bees, and not to humans; it helps to guide bees to the 
center of the flower, thus making the pollination process more efficient. The 
pollen sticks to the bees’ fuzzy hair, and when the bee visits another flower, 


some of the pollen is transferred to the second flower. Recently, there have 
been many reports about the declining population of honeybees. Many 
flowers will remain unpollinated and not bear seed if honeybees disappear. 
The impact on commercial fruit growers could be devastating. 


Insects, such as bees, are 
important agents of pollination. 
(credit: photo by D. A. Rintoul) 


Many flies are attracted to flowers that have a decaying smell or an odor of 
rotting flesh. These flowers, which produce nectar, usually have dull colors, 
such as brown or purple. They are found on the corpse flower or voodoo 
lily (Amorphophallus), dragon arum (Dracunculus), and carrion flower 
(Stapleia, Rafflesia). The nectar provides energy, whereas the pollen 
provides protein. Wasps are also important insect pollinators, and pollinate 
many species of figs. 


Butterflies, such as the monarch, pollinate many garden flowers and 
wildflowers, which usually occur in clusters. These flowers are brightly 
colored, have a strong fragrance, are open during the day, and have nectar 
guides to make access to nectar easier. The pollen is picked up and carried 
on the butterfly’s limbs. Moths, on the other hand, pollinate flowers during 
the late afternoon and night. The flowers pollinated by moths are pale or 
white and are flat, enabling the moths to land. One well-studied example of 
a moth-pollinated plant is the yucca plant, which is pollinated by the yucca 
moth. The shape of the flower and moth have adapted in such a way as to 
allow successful pollination. The moth deposits pollen on the sticky stigma 
for fertilization to occur later. The female moth also deposits eggs into the 
ovary. As the eggs develop into larvae, they obtain food from the flower 
and developing seeds. Thus, both the insect and flower benefit from each 
other in this symbiotic relationship. The corn earworm moth and Gaura 
plant have a similar relationship ((link]). 


A corn earworm sips nectar from a 
night-blooming Gaura plant. 
(credit: Juan Lopez, USDA ARS) 


Pollination by Bats 


In the tropics and deserts, bats are often the pollinators of nocturnal flowers 
such as agave, guava, and morning glory. The flowers are usually large and 
white or pale-colored; thus, they can be distinguished from the dark 
surroundings at night. The flowers have a strong, fruity, or musky fragrance 
and produce large amounts of nectar. They are naturally large and wide- 
mouthed to accommodate the head of the bat. As the bats seek the nectar, 
their faces and heads become covered with pollen, which is then transferred 
to the next flower. 


Pollination by Birds 


Many species of small birds, such as hummingbirds and the Australasian 
birds known as honeyeaters ([link]), are pollinators for a wide variety of 
plants. Flowers visited by birds are usually sturdy and are oriented in such a 
way as to allow the birds to stay near the flower without getting their wings 
entangled in the nearby flowers. The flower typically has a curved, tubular 
shape, which allows access for the bird’s beak. Brightly colored, odorless 
flowers that are open during the day are pollinated by birds. As a bird seeks 
energy-rich nectar, pollen is deposited on the bird’s head and neck and is 
then transferred to the next flower it visits. Botanists have been known to 
determine the range of extinct plants by collecting and identifying pollen 
from 200-year-old bird specimens from the same site. 


Hummingbirds (shown at left) have adaptations (long beaks, ability to 
hover, etc.) that allow them to reach the nectar of certain tubular 
flowers, but in the process they can collect pollen on their beaks or 
heads and then transfer it to another flower. Other birds, like the Tui 
(at right), a honeyeater found in New Zealand, also collect pollen on 
their foreheads as they forage on nectar. (credit: photos by D. A. 
Rintoul) 


Pollination by Wind 


Most species of conifers, and many angiosperms, such as grasses, maples 
and oaks, are pollinated by wind. Pine cones are brown and unscented, 
while the flowers of wind-pollinated angiosperm species are usually green, 
small, may have small or no petals, and produce large amounts of pollen. 
Unlike the typical insect-pollinated flowers, flowers adapted to pollination 
by wind do not produce nectar or scent. In wind-pollinated species, the 
microsporangia hang out of the flower, and, as the wind blows, the 
lightweight pollen is carried with it ([link]). The flowers usually emerge 
early in the spring, before the leaves, so that the leaves do not block the 


movement of the wind. The pollen is deposited on the exposed feathery 
stigma of the flower ((link]). 


A person knocks pollen from a 
pine tree. 


These male (a) and female (b) catkins are from the goat 

willow tree (Salix caprea). Note how both structures are 

light and feathery to better disperse and catch the wind- 
blown pollen. 


Pollination by Water 


Some weeds, such as Australian sea grass and pond weeds, are pollinated 
by water. The pollen floats on water, and when it comes into contact with 
the flower, it is deposited inside the flower. 


Note: 

Evolution Connection 

Pollination by Deception 

Orchids are highly valued flowers, with many rare varieties ([link]). They 
grow in a range of specific habitats, mainly in the tropics of Asia, South 
America, and Central America. At least 25,000 species of orchids have 
been identified. 


Certain orchids use food deception 


or sexual deception to attract 
pollinators. Shown here is a bee 
orchid (Ophrys apifera). (credit: 
David Evans) 


Flowers often attract pollinators with food rewards, in the form of nectar. 
However, some species of orchid are an exception to this standard: they 
have evolved different ways to attract the desired pollinators. They use a 
method known as food deception, in which bright colors and perfumes are 
offered, but no food. Anacamptis morio, commonly known as the green- 
winged orchid, bears bright purple flowers and emits a strong scent. The 
bumblebee, its main pollinator, is attracted to the flower because of the 
strong scent—which usually indicates food for a bee—and in the process, 
picks up the pollen to be transported to another flower. 

Other orchids use sexual deception. Chiloglottis trapeziformis emits a 
compound that smells the same as the pheromone emitted by a female 
wasp to attract male wasps. The male wasp is attracted to the scent, lands 
on the orchid flower, and in the process, transfers pollen. Some orchids, 
like the Australian hammer orchid, use scent as well as visual trickery in 
yet another sexual deception strategy to attract wasps. The flower of this 
orchid mimics the appearance of a female wasp and emits a pheromone. 
The male wasp tries to mate with what appears to be a female wasp, and in 
the process, picks up pollen, which it then transfers to the next counterfeit 
mate. 


Double Fertilization 


After pollen is deposited on the stigma, it must germinate and grow through 
the style to reach the ovule. The microspores, or the pollen, contain two 
cells: the pollen tube cell and the generative cell. The pollen tube cell grows 
into a pollen tube through which the generative cell travels. The 
germination of the pollen tube requires water, oxygen, and certain chemical 
signals. As it travels through the style to reach the embryo sac, the pollen 
tube’s growth is supported by the tissues of the style. In the meantime, if the 


generative cell has not already split into two cells, it now divides to form 
two sperm cells. The pollen tube is guided by the chemicals secreted by the 
synergids present in the embryo sac, and it enters the ovule sac through the 
micropyle. Of the two sperm cells, one sperm fertilizes the egg cell, 
forming a diploid zygote; the other sperm fuses with the two polar nuclei, 
forming a triploid cell that develops into the endosperm. Together, these 
two fertilization events in angiosperms are known as double fertilization 
({link]). After fertilization is complete, no other sperm can enter. The 
fertilized ovule forms the seed, whereas the tissues of the ovary become the 
fruit, usually enveloping the seed. 


Pollen grain 


Micropyle 
Egg 


Stigma 
9 Pollen tube 


Polar 


Sperm ; 
nuclei 


Style Synergids 
Egg 
_— _— Polar 
nuclei 
Ovules Sperm 
Ovary nuclei 
Antipodals 
Embryo sac 
The pollen grain adheres to The pollen tube cell grows The pollen tube penetrates One of the sperm fertilizes 
the stigma, which contains into the style. The generative an opening in the ovule the egg to form the diploid 
two cells: a generative cell Cell travels inside the pollen called a micropyle. zygote. The other sperm 
and a tube cell. tube. It divides to form two fertilizes two polar nuclei to 


sperm. form the triploid endosperm, 
which will become a food 
source for the growing 
embryo. 


In angiosperms, one sperm fertilizes the egg to form the 2n 
zygote, and the other sperm fertilizes the central cell to form 
the 3n endosperm. This is called a double fertilization. 


After fertilization, the zygote divides to form two cells: the upper cell, or 
terminal cell, and the lower, or basal, cell. The division of the basal cell 
gives rise to the suspensor, which eventually makes connection with the 
maternal tissue. The suspensor provides a route for nutrition to be 
transported from the mother plant to the growing embryo. The terminal cell 


also divides, giving rise to a globular-shaped proembryo ([link]a). In 
eudicots, the developing embryo has a heart shape, due to the presence of 
the two rudimentary cotyledons ([link]b). In non-endospermic eudicots, 
such as Capsella bursa, the endosperm develops initially, but is then 
digested, and the food reserves are moved into the two cotyledons. As the 
embryo and cotyledons enlarge, they run out of room inside the developing 
seed, and are forced to bend ([link]c). Ultimately, the embryo and 
cotyledons fill the seed ([link]d), and the seed is ready for dispersal. 
Embryonic development is suspended after some time, and growth is 
resumed only when the seed germinates. The developing seedling will rely 
on the food reserves stored in the cotyledons until the first set of leaves 
begin photosynthesis. 


Cotyledons 


werent s5%s = 
> 
ee 


~ = 2% 
a a 


Proembryo 
Embryo 
Suspensor 


ao 
Liess 


Suspensor 


Basal cell 
Basal cell 


Short meristem 
Endosperm 
Cotyledons 
Seed coat 


Embryonic 
axis Cotyledons 


Root meristem 


Shown are the stages of embryo 
development in the ovule of a shepherd’s 
purse (Capsella bursa). After fertilization, 
the zygote divides to form an upper terminal 
cell and a lower basal cell. (a) In the first 
stage of development, the terminal cell 
divides, forming a globular pro-embryo. The 
basal cell also divides, giving rise to the 
suspensor. (b) In the second stage, the 
developing embryo has a heart shape due to 
the presence of cotyledons. (c) In the third 
stage, the growing embryo runs out of room 
and starts to bend. (d) Eventually, it 
completely fills the seed. (credit: 
modification of work by Robert R. Wise; 
scale-bar data from Matt Russell) 


Development of the Seed 


The mature ovule develops into the seed. A typical seed contains a seed 
coat, cotyledons, endosperm, and a single embryo ([link]). 


Endosperm 


Epicotyl 


Hypocoty| 

Radicle Embryo 
Cotyledon 
Seed coat 


Bean seed Corn seed 
(Eudicot) (Monocot) 


The structures of eudicot and monocot seeds 
are shown. Eudicots (left) have two 
cotyledons. Monocots, such as corn (right), 
have one cotyledon, called the scutellum; it 
channels nutrition to the growing embryo. 
Both monocot and eudicot embryos have a 
plumule that forms the leaves, a hypocotyl 
that forms the stem, and a radicle that forms 
the root. The embryonic axis comprises 
everything between the plumule and the 
radicle, not including the cotyledon(s). 


The storage of food reserves in angiosperm seeds differs between monocots 
and eudicots. In monocots, such as corn and wheat, the single cotyledon is 
connected directly to the embryo via vascular tissue (xylem and phloem). 
Food reserves are stored in the large endosperm. Upon germination, 
enzymes are secreted by the aleurone, a single layer of cells just inside the 
seed coat that surrounds the endosperm and embryo. The enzymes degrade 
the stored carbohydrates, proteins and lipids, the products of which are 
absorbed by the cotyledon and transported to the developing embryo. 
Therefore, the cotyledon can be seen to be an absorptive organ, not a 
storage organ. 


The two cotyledons in the eudicot seed also have vascular connections to 
the embryo. In endospermic eudicots, the food reserves are stored in the 
endosperm. During germination, the two cotyledons therefore act as 
absorptive organs to take up the enzymatically released food reserves, much 
like in monocots (monocots, by definition, also have endospermic seeds). 
Tobacco (Nicotiana tabaccum), tomato (Solanum lycopersicum), and 
pepper (Capsicum annuum) are examples of endospermic eudicots. In non- 
endospermic eudicots, the triploid endosperm develops normally following 
double fertilization, but the endosperm food reserves are quickly 
remobilized and moved into the developing cotyledon for storage. The two 
halves of a peanut seed (Arachis hypogaea) and the split peas (Pisum 


sativum) of split pea soup are individual cotyledons loaded with food 
reserves. 


The seed, along with the ovule, is protected by a seed coat that is formed 
from the integuments of the ovule sac. The embryo consists of three parts: 
the plumule, the radicle, and the hypocotyl. The portion of the embryo 
between the cotyledon attachment point and the radicle is known as the 
hypocotyl (hypocotyl means “below the cotyledons”). The embryo 
terminates in a radicle (the embryonic root), which is the region from 
which the root will develop. In eudicots, the hypocotyls extend above 
ground, giving rise to the stem of the plant. In monocots, the hypocotyl 
does not show above ground because monocots do not exhibit stem 
elongation. The part of the embryonic axis that projects above the 
cotyledons is known as the epicotyl. The plumule is composed of the 
epicotyl, young leaves, and the shoot apical meristem. 


Upon germination in eudicot seeds ({link]), the epicotyl is shaped like a 
hook with the plumule pointing downwards. This shape is called the 
plumule hook, and it persists as long as germination proceeds in the dark. 
Therefore, as the epicotyl pushes through the tough and abrasive soil, the 
plumule is protected from damage. Upon exposure to light, the hypocotyl 
hook straightens out, the young foliage leaves face the sun and expand, and 
the epicotyl continues to elongate. During this time, the radicle is also 
growing and producing the primary root. As it grows downward to form the 
tap root, lateral roots branch off to all sides, producing the typical eudicot 
tap root system. 


Epicotyl 


Hypoc otyl between cotyledons Cotyledo ns 


Seed coat 


J 


a Seed coat 


Radicle 
Primary 
Root 


As this eudicot bean seed germinates, the primary root, or radicle, 
emerges first, followed by the hypocotyl and cotyledons. Work by 
Robert A. Bear 


As a monocot seed germinates ([link]), the primary root emerges, protected 
by the root-tip covering: the coleorhiza. Next, the primary shoot emerges, 
protected by the coleoptile: the covering of the shoot tip. Upon exposure to 
light (i.e. when the plumule has exited the soil and the protective coleoptile 
is no longer needed), elongation of the coleoptile ceases and the leaves 
expand and unfold. At the other end of the embryon, the primary root soon 
dies, while other, adventitious roots (roots that do not arise from the usual 
place — i.e. the root) emerge from the base of the stem. This gives the 
monocot a fibrous root system. 


Primary 
root 


Adventitious roots 


As this monocot corn seed germinates, the primary root, or radicle, 
emerges first, followed by the primary shoot, or coleoptile, and the 
adventitious roots. Work by Robert A. Bear 


Seed Germination 


Many mature seeds enter a period of inactivity, or extremely low metabolic 
activity: a process known as dormancy, which may last for months, years or 
even centuries. Dormancy helps keep seeds viable during unfavorable 
conditions. Upon a return to favorable conditions, seed germination takes 
place. Favorable conditions could be as diverse as moisture, light, cold, fire, 
or chemical treatments. After heavy rains, many new seedlings emerge. 


Forest fires also lead to the emergence of new seedlings. Some seeds 
require vernalization (cold treatment) before they can germinate. This 
guarantees that seeds produced by plants in temperate climates will not 
germinate until the spring. Plants growing in hot climates may have seeds 
that need a heat treatment in order to germinate, to avoid germination in the 
hot, dry summers. In many seeds, the presence of a thick seed coat retards 
the ability to germinate. Scarification, which includes mechanical or 
chemical processes to soften the seed coat, is often employed before 
germination. Presoaking in hot water, or passing through an acid 
environment, such as an animal’s digestive tract, may also be employed. 


Depending on seed size, the time taken for a seedling to emerge may vary. 
Species with large seeds have enough food reserves to germinate deep 
below ground, and still extend their epicoty] all the way to the soil surface. 
Seeds of small-seeded species usually require light as a germination cue. 
This ensures the seeds only germinate at or near the soil surface (where the 
light is greatest). If they were to germinate too far underneath the surface, 
the developing seedling would not have enough food reserves to reach the 
sunlight. 


Development of Fruit and Fruit Types 


After fertilization, the ovary of the flower usually develops into the fruit. 
Fruits are usually associated with having a sweet taste; however, not all 
fruits are sweet. Botanically, the term “fruit” is used for a ripened ovary. In 
most cases, flowers in which fertilization has taken place will develop into 
fruits, and flowers in which fertilization has not taken place will not. Some 
fruits develop from the ovary and are known as true fruits, whereas others 
develop from other parts of the female gametophyte and are known as 
accessory fruits. The fruit encloses the seeds and the developing embryo, 
thereby providing it with protection. Fruits are of many types, depending on 
their origin and texture. The sweet tissue of the blackberry, the red flesh of 
the tomato, the shell of the peanut, and the hull of corn (the tough, thin part 
that gets stuck in your teeth when you eat popcorn) are all fruits. As the 
fruit matures, the seeds also mature. 


Fruits may be classified as simple, aggregate, multiple, or accessory, 
depending on their origin ([link]). If the fruit develops from a single carpel 
or fused carpels of a single ovary, it is known as a simple fruit, as seen in 
nuts and beans. An aggregate fruit is one that develops from more than one 
carpel, but all are in the same flower: the mature carpels fuse together to 
form the entire fruit, as seen in the raspberry. Multiple fruit develops from 
an inflorescence or a cluster of flowers. An example is the pineapple, where 
the flowers fuse together to form the fruit. Accessory fruits (sometimes 
called false fruits) are not derived from the ovary, but from another part of 
the flower, such as the receptacle (strawberry) or the hypanthium (apples 
and pears). 


Simple fruit 


Aggregate fruit 


Multiple fruit 


There are four main types of fruits. Simple 
fruits, such as these nuts, are derived from a 


single ovary. Aggregate fruits, like 
raspberries, form from many carpels that 
fuse together. Multiple fruits, such as 
pineapple, form from a cluster of flowers 
called an inflorescence. Accessory fruit, like 
the apple, are formed from a part of the plant 
other than the ovary. (credit "nuts": 
modification of work by Petr Kratochvil; 
credit "raspberries": modification of work 
by Cory Zanker; credit "pineapple": 
modification of work by Howie Le; credit 
"apple": modification of work by Paolo 
Neo) 


Fruits generally have three parts: the exocarp (the outermost skin or 
covering), the mesocarp (middle part of the fruit), and the endocarp (the 
inner part of the fruit). Together, all three are known as the pericarp. The 
mesocarp is usually the fleshy, edible part of the fruit; however, in some 
fruits, such as the almond, the endocarp is the edible part. In many fruits, 
two or all three of the layers are fused, and are indistinguishable at maturity. 
Fruits can be dry or fleshy. Furthermore, fruits can be divided into dehiscent 
or indehiscent types. Dehiscent fruits, such as peas, readily release their 
seeds, while indehiscent fruits, like peaches, rely on decay to release their 
seeds. 


Fruit and Seed Dispersal 


The fruit has a single purpose: seed dispersal. Seeds contained within fruits 
need to be dispersed far from the mother plant, so they may find favorable 
and less competitive conditions in which to germinate and grow. 


Some fruit have built-in mechanisms so they can disperse by themselves, 
whereas others require the help of agents like wind, water, and animals 
({link]). Modifications in seed structure, composition, and size help in 
dispersal. Wind-dispersed fruit are lightweight and may have wing-like 


appendages that allow them to be carried by the wind. Some have a 
parachute-like structure to keep them afloat. Some fruits—for example, the 
dandelion—have hairy, nearly weightless structures that are suited to 
dispersal by wind. 


Seeds dispersed by water are contained in light and buoyant fruit, giving 
them the ability to float. Coconuts are well known for their ability to float 
on water to reach land where they can germinate. Similarly, willow and 
silver birches produce lightweight fruit that can float on water. 


Animals and birds eat fruits, and the seeds that are not digested are excreted 
in their droppings some distance away. Some animals, like squirrels, bury 
seed-containing fruits for later use; if the squirrel does not find its stash of 
fruit, and if conditions are favorable, the seeds germinate. Some fruits, like 
the cocklebur, have hooks or sticky structures that stick to an animal's coat 
and are then transported to another place. Humans also play a big role in 
dispersing seeds when they carry fruits to new places and throw away the 
inedible part that contains the seeds. 


All of the above mechanisms allow for seeds to be dispersed through space, 
much like an animal’s offspring can move to a new location. Seed 
dormancy, which was described earlier, allows plants to disperse their 
progeny through time: something animals cannot do. Dormant seeds can 
wait months, years, or even decades for the proper conditions for 
germination and propagation of the species. 


Fruits and seeds are dispersed by various 
means. (a) Dandelion seeds are dispersed 
by wind, the (b) coconut seed is dispersed 
by water, and the (c) acorn is dispersed by 


animals that cache and then forget it. 
(credit a: modification of work by 
"Rosendahl"/Flickr; credit b: modification 
of work by Shine Oa; credit c: 
modification of work by Paolo Neo) 


Root and Leaf Structure 


Introduction 

"A tree nowhere offers a straight line or a regular curve, but who doubts 
that root, trunk, boughs, and leaves embody geometry?" George Iles, in 
Canadian Stories (1918) 


We all recognize roots, trunks and leaves as parts of a plant. In this chapter 
you will learn a bit more about those structures, and how they are parts of 
plant organ systems. 


Plant Organ Systems 


In plants, just as in animals, similar cells working together form a tissue. 
When different types of tissues work together to perform a unique function, 
they form an organ; organs working together form organ systems. Vascular 
plants have two distinct organ systems: a shoot system, and a root system. 
The shoot system consists of two portions: the vegetative (non- 
reproductive) parts of the plant, such as the leaves and the stems, and the 
reproductive parts of the plant, which include flowers and fruits. The shoot 
system generally grows above ground, where it absorbs the light needed for 
photosynthesis. The root system, which supports the plants and absorbs 
water and minerals, is usually underground. [link] shows the organ systems 
of a typical plant. 


Reproductive 


Vegetative 


Shoot system 


Root system 


The shoot system of a plant 
consists of leaves, stems, flowers, 
and fruits. The root system 
anchors the plant while absorbing 
water and minerals from the soil. 


Roots 


The roots of seed plants have three major functions: anchoring the plant to 
the soil, absorbing water and minerals and transporting them upwards, and 
storing the products of photosynthesis. Some roots are modified to absorb 
moisture and exchange gases. Most roots are underground. Some plants, 
however, also have adventitious roots, which emerge above the ground 
from the shoot. 


Types of Root Systems 


Root systems are mainly of two types ([link]). Eudicots have a tap root 
system, while monocots have a fibrous root system. A tap root system has 
a main root that grows down vertically, and from which many smaller 
lateral roots arise. Dandelions are a good example; their tap roots usually 
break off when trying to pull these weeds, and they can regrow another 
shoot from the remaining root). A tap root system penetrates deep into the 
soil. In contrast, a fibrous root system is located closer to the soil surface, 
and forms a dense network of roots that also helps prevent soil erosion 
(lawn grasses are a good example, as are wheat, rice, and corn). Some 
plants have a combination of tap roots and fibrous roots. Plants that grow in 
dry areas often have deep root systems, whereas plants growing in areas 
with abundant water are likely to have shallower root systems. 


(a) Tap root systems have a main root that 
grows down, while (b) fibrous root systems 
consist of many small roots. (credit b: 
modification of work by “Austen 
Squarepants”/Flickr) 


Root Growth and Anatomy 


Root growth begins with seed germination. When the plant embryo emerges 
from the seed, the radicle of the embryo forms the root system. The tip of 
the root is protected by the root cap, a structure exclusive to roots and 
unlike any other plant structure. The root cap is continuously replaced 
because it gets damaged easily as the root pushes through soil. The root tip 
can be divided into three zones: a zone of cell division, a zone of 
elongation, and a zone of maturation and differentiation ({link]). The zone 
of cell division is closest to the root tip; it is made up of the actively 
dividing cells of the root meristem. The zone of elongation is where the 
newly formed cells increase in length, thereby lengthening the root. 
Beginning at the first root hair is the zone of cell maturation where the root 
cells begin to differentiate into special cell types. All three zones are in the 
first centimeter or so of the root tip. 


Vascular 
cylinder 


Root hair 


Area of 
maturation 


Area of 
elongation 


Apical 


meristem 
Area of 


cell division 
Root cap 


A longitudinal view of the 
root reveals the zones of cell 
division, elongation, and 
maturation. Cell division 
occurs in the apical meristem. 


The root has an outer layer of cells called the epidermis, which surrounds 
areas of ground tissue and vascular tissue. The epidermis provides 
protection and helps in absorption. Root hairs, which are extensions of root 
epidermal cells, increase the surface area of the root, greatly contributing to 
the absorption of water and minerals. 


Inside the root, the ground tissue forms two regions: the cortex and the pith 
({link]). Compared to stems, roots have lots of cortex and little pith. Both 
regions include cells that store photosynthetic products. The cortex is 
between the epidermis and the vascular tissue, whereas the pith lies 
between the vascular tissue and the center of the root. 


Exodermis 
(sclerenchyma) Epidermis Phloem 


Cortex Pericycle Endodermis Root hairs 
(parenchyma cells) 


Staining reveals different cell 
types in this light micrograph of a 
wheat (Triticum) root cross 
section. Sclerenchyma cells of the 
exodermis and xylem cells stain 
red, and phloem cells stain blue. 
Other cell types stain black. The 
stele, or vascular tissue, is the area 
inside endodermis (indicated by a 
green ring). Root hairs are visible 
outside the epidermis. (credit: 
scale-bar data from Matt Russell) 


The vascular tissue in the root is arranged in the inner portion of the root, 
which is called the vascular cylinder ({link]). A layer of cells known as the 
endodermis separates the vascular tissue from the ground tissue in the 
outer portion of the root. The endodermis is exclusive to roots, and serves 
as a checkpoint for materials entering the root’s vascular system. A waxy 
substance called suberin is present on the walls of the endodermal cells. 
This waxy region, known as the Casparian strip, forces water and solutes 
to cross the plasma membranes of endodermal cells instead of slipping 
between the cells. This ensures that only materials required by the root pass 
through the endodermis, while toxic substances and pathogens are generally 
excluded. The outermost cell layer of the root’s vascular tissue is the 
pericycle, an area that can give rise to lateral roots. In eudicot roots, the 
xylem and phloem are arranged alternately in an X shape, whereas in 
monocot roots, the vascular tissue is arranged in a ring around the pith. 


Eudicot root Monocot root 


Epidermis ee es Pith 


Pericycle 


Endodermis 


In (left) typical eudicots, the vascular tissue forms 
an X shape in the center of the root. In (right) 


typical monocots, the phloem cells and the larger 
xylem cells form a characteristic ring around the 
central pith. 


Root Modifications 


Root structures may be modified for specific purposes. For example, some 
roots are bulbous and store starch. Aerial roots and prop roots are two forms 
of aboveground roots that provide additional support to anchor the plant. 
Tap roots, such as carrots, turnips, and beets, are examples of roots that are 
modified for food storage ([link]). 


Many vegetables are 
modified roots. 


Epiphytic roots enable a plant to grow on another plant. For example, the 

epiphytic roots of orchids develop a spongy tissue to absorb moisture. The 
banyan tree (Ficus sp.) begins as an epiphyte, germinating in the branches 
of a host tree; aerial roots develop from the branches and eventually reach 
the ground, providing additional support ([link]). In screwpine (Pandanus 


sp.), a palm-like tree that grows in sandy tropical soils, aboveground prop 
roots develop from the nodes to provide additional support. 


The (a) banyan tree, also known as the strangler fig, 
begins life as an epiphyte in a host tree. Aerial roots 
extend to the ground and support the growing plant, 
which eventually strangles the host tree. The (b) 
screwpine develops aboveground roots that help 
support the plant in sandy soils. (credit a: modification 
of work by "psyberartist"/Flickr; credit b: modification 
of work by David Eikhoff) 


Leaves 


Leaves are the main sites for photosynthesis: the process by which plants 
synthesize food. Most leaves are usually green, due to the presence of 
chlorophyll in the leaf cells. However, some leaves may have different 
colors, caused by other plant pigments that mask the green chlorophyll. 


The thickness, shape, and size of leaves are adapted to the environment. 
Each variation helps a plant species maximize its chances of survival in a 
particular habitat. Usually, the leaves of plants growing in tropical 
rainforests have larger surface areas than those of plants growing in deserts 


or very cold conditions, which are likely to have a smaller surface area to 
minimize water loss. 


Structure of a Typical Leaf 


Each leaf typically has a leaf blade called the lamina, which is also the 
widest part of the leaf. Some leaves are attached to the plant stem by a 
petiole. Leaves that do not have a petiole and are directly attached to the 
plant stem are called sessile leaves. Small green appendages usually found 
at the base of the petiole are known as stipules. Most leaves have a midrib, 
which travels the length of the leaf and branches to each side to produce 
veins of vascular tissue. The edge of the leaf is called the margin. [link] 
shows the structure of a typical eudicot leaf. 


Deceptively simple in appearance, 
a leaf is a highly efficient 
structure. 


Within each leaf, the vascular tissue forms veins. The arrangement of veins 
in a leaf is called the venation pattern. Monocots and eudicots differ in their 
patterns of venation ([link]). Monocots have parallel venation; the veins run 
in straight lines across the length of the leaf without converging at a point. 
In eudicots, however, the veins of the leaf have a net-like appearance, 
forming a pattern known as reticulate venation. One extant plant, the 
Ginkgo biloba, has dichotomous venation where the veins fork. 


(a) (b) (c) 


(a) Tulip (Tulipa), a monocot, has leaves with 
parallel venation. The netlike venation in this (b) 
linden (Tilia cordata) leaf distinguishes it as a 
eudicot. The (c) Ginkgo biloba tree has dichotomous 
venation. (credit a photo: modification of work by 
“Drewboy64”/Wikimedia Commons; credit b photo: 
modification of work by Roger Griffith; credit c 
photo: modification of work by 
"geishaboy500"/Flickr; credit abc illustrations: 
modification of work by Agnieszka Kwiecien) 


Leaf Structure and Function 


The outermost layer of the leaf is the epidermis; it is present on both sides 
of the leaf and is called the upper and lower epidermis, respectively. The 
epidermis helps in the regulation of gas exchange. It contains stomata 
({link]): openings through which the exchange of gases takes place. Two 
guard cells surround each stoma, regulating its opening and closing. 


Visualized at 500x with a scanning electron microscope, several 
stomata are Clearly visible on (a) the surface of this sumac (Rhus 
glabra) leaf. At 5,000x magnification, the guard cells of (b) a 
single stoma from lyre-leaved sand cress (Arabidopsis lyrata) 
have the appearance of lips that surround the opening. In this (c) 
light micrograph cross-section of an A. lyrata leaf, the guard cell 
pair is visible along with the large, sub-stomatal air space in the 
leaf. (credit: modification of work by Robert R. Wise; part c scale- 
bar data from Matt Russell) 


When a plant has sufficient amount of water and sunlight, guard cells 
accumulate potassium (K*) ions, and water flows into the guard cells by 
osmosis. The movement of water into the guard cells causes the cells to 
swell and become turgid. As the cells become more turgid, the inner thick 
cell wall does not stretch as much as the thin outer cell wall, and this causes 
a space to form between the two guard cells opening the stoma. When the 
plant closes that stoma, K* ions leave the guard cells, and water follows by 
osmosis. The movement of water out of the guard cells causes the cells to 


shrink and become flaccid thereby closing the stoma. [link] is an illustration 
of how guard cells open and close the stoma. 


Closed Stomata 


Flaccid guard cells 


cell wall cell wall 


Open Stomata 
Turgid guard cells 


Thick Thin 
cell wall cell wall 


The movement of potassium ions (K*) into and 
out of the guard cells allows the plant to either 
open or close its stomata. Work by Robert A. 
Bear 


The movement of K” ions into or out of the guard cell as currently 
hypothesized is a passive process and related to the active transport of H* 
ions in the opposite direction of the movement of the K* ions. So, when H* 
ions are actively pumped out of the guard cell, K* ions move into the guard 
cell passively flowing down an electrical gradient created by the H” ions. 
Since the plant uses energy to open and close the stomata, the benefits of 
regulating the opening and closing of the stomata are greater than the 
energy expenditure of moving ions into and out of the guard cells. Plants 
actively regulate the movement of these ions and can respond rapidly to 
changes in the amount of sunlight, relative humidity and carbon dioxide. 


The epidermis is usually one cell layer thick; however, in plants that grow 
in very hot or very cold conditions, the epidermis may be several layers 
thick to protect against excessive water loss from transpiration. A waxy 
layer known as the cuticle covers the leaves of all plant species. The cuticle 
reduces the rate of water loss from the leaf surface. Other leaves may have 
small hairs (trichomes) on the leaf surface. Trichomes help to deter 
herbivory by restricting insect movements, or by storing toxic or bad-tasting 
compounds; they can also reduce the rate of transpiration by blocking air 
flow across the leaf surface ([link]). 


a 


Ie 


~é 


_ 125 pm 


gt 


Trichomes give leaves a fuzzy appearance as in this (a) sundew 
(Drosera sp.). Leaf trichomes include (b) branched trichomes 
on the leaf of Arabidopsis lyrata and (c) multibranched 
trichomes on a mature Quercus marilandica leaf. (credit a: 
John Freeland; credit b, c: modification of work by Robert R. 
Wise; scale-bar data from Matt Russell) 


Below the epidermis of eudicot leaves are layers of cells known as the 
mesophyll, or “middle leaf.” The mesophyll of most leaves typically 
contains two arrangements of parenchyma cells: the palisade parenchyma 
and spongy parenchyma ([link]). The palisade parenchyma (also called the 
palisade mesophyll) has column-shaped, tightly packed cells, and may be 
present in one, two, or three layers. Below the palisade parenchyma are 
loosely arranged cells of an irregular shape. These are the cells of the 
spongy parenchyma (or spongy mesophyll). The air space found between 
the spongy parenchyma cells allows gaseous exchange between the leaf and 
the outside atmosphere through the stomata. In aquatic plants, the 
intercellular spaces in the spongy parenchyma help the leaf float. Both 
layers of the mesophyll contain many chloroplasts. Guard cells are the only 
epidermal cells to contain chloroplasts. 


Cuticle 
Upper 
epidermis 


Palisade parenchyma 


Mesophyll 


Spongy parenchyma 


Lower 
epidermis 


Cuticle 
Guard cells 


200 um 


In the (a) leaf drawing, the central 
mesophyll is sandwiched between an 
upper and lower epidermis. The 
mesophyll has two layers: an upper 
palisade layer comprised of tightly 
packed, columnar cells, and a lower 
spongy layer, comprised of loosely 
packed, irregularly shaped cells. Stomata 
on the leaf underside allow gas 
exchange. A waxy cuticle covers all 
aerial surfaces of land plants to minimize 
water loss. These leaf layers are clearly 
visible in the (b) scanning electron 
micrograph. The numerous small bumps 


in the palisade parenchyma cells are 
chloroplasts. Chloroplasts are also 
present in the spongy parenchyma, but 
are not as obvious. The bumps 
protruding from the lower surface of the 
leave are glandular trichomes, which 
differ in structure from the stalked 
trichomes in [link]. (credit b: 
modification of work by Robert R. Wise) 


Like the stem, the leaf contains vascular bundles composed of xylem and 
phloem ({link]). The xylem consists of tracheids and vessels, which 
transport water and minerals to the leaves. The phloem transports the 
photosynthetic products from the leaf to the other parts of the plant. A 
single vascular bundle, no matter how large or small, always contains both 
xylem and phloem tissues. 


This scanning electron micrograph 
shows xylem and phloem in the leaf 
vascular bundle from the lyre-leaved 

sand cress (Arabidopsis lyrata). 


(credit: modification of work by 
Robert R. Wise; scale-bar data from 
Matt Russell) 


Leaf Adaptations 


Coniferous plant species that thrive in cold environments, like spruce, fir, 
and pine, have leaves that are reduced in size and needle-like in appearance. 
These needle-like leaves have sunken stomata and a smaller surface area: 
two attributes that aid in reducing water loss. In hot climates, plants such as 
cacti have succulent leaves that help to conserve water. Many aquatic plants 
have leaves with wide lamina that can float on the surface of the water, and 
a thick waxy cuticle on the leaf surface that repels water. 


Note: 

Evolution Connection 

Plant Adaptations in Resource-Deficient Environments 

Roots, stems, and leaves are structured to ensure that a plant can obtain the 
required resources of sunlight, water, soil nutrients, carbon dioxide and 
oxygen. Some remarkable adaptations have evolved to enable plant species 
to thrive in less than ideal habitats, where one or more of these resources is 
in short supply. 

In tropical rainforests, light is often scarce, since many trees and plants 
grow Close together and block much of the sunlight from reaching the 
forest floor. Many tropical plant species have exceptionally broad leaves to 
maximize the capture of sunlight. Other species are epiphytes: plants that 
grow on other plants that serve as a physical support. Such plants are able 
to grow high up in the canopy atop the branches of other trees, where 
sunlight is more plentiful. Epiphytes live on rain and minerals collected in 
the branches and leaves of the supporting plant. Bromeliads (members of 
the pineapple family), ferns, and orchids are examples of tropical epiphytes 


({link]). Many epiphytes have specialized tissues that enable them to 
efficiently capture and store water. 


x 


One of the most well 
known bromeliads is 
Spanish moss (Tillandsia 
usneoides), seen here in 
an Oak tree. (credit: 
Kristine Paulus) 


Some plants have special adaptations that help them to survive in nutrient- 
poor environments. Carnivorous plants, such as the Venus flytrap and the 
pitcher plant ([link]), grow in bogs where the soil is low in nitrogen. In 
these plants, leaves are modified to capture insects. The insect-capturing 
leaves may have evolved to provide these plants with a supplementary 
source of much-needed nitrogen. 


(a) (b) 


The (a) Venus flytrap has modified leaves that can 
capture insects. When an unlucky insect touches 
the trigger hairs inside the leaf, the trap suddenly 

closes. The opening of the (b) pitcher plant is lined 

with a slippery wax. Insects crawling on the lip 
slip and fall into a pool of water in the bottom of 
the pitcher, where they are digested by bacteria. 
The plant then absorbs the smaller molecules. 
(credit a: modification of work by Peter Shanks; 
credit b: modification of work by Tim Mansfield) 


Many swamp plants have adaptations that enable them to thrive in wet 
areas, where their roots grow submerged underwater. In these aquatic 
areas, the soil is unstable and little oxygen is available to reach the roots. 
Trees such as mangroves (Rhizophora sp.) growing in coastal waters 
produce aboveground roots that help support the tree ([link]). Some species 
of mangroves, as well as cypress trees, have pneumatophores: upward- 
growing roots containing pores and pockets of tissue specialized for gas 
exchange. Wild rice is an aquatic plant with large air spaces in the root 
cortex. The air-filled tissue—called aerenchyma—provides a path for 
oxygen to diffuse down to the root tips, which are embedded in oxygen- 
poor bottom sediments. 


(a) (b) (c) 


The branches of (a) mangrove trees develop aerial roots, which 
descend to the ground and help to anchor the trees. (b) Cypress 
trees and some mangrove species have upward-growing roots 
called pneumatophores that are involved in gas exchange. 
Aquatic plants such as (c) wild rice have large spaces in the 
root cortex called aerenchyma, visualized here using scanning 
electron microscopy. (credit a: modification of work by 
Roberto Verzo; credit b: modification of work by Duane 
Burdick; credit c: modification of work by Robert R. Wise) 


Transport of Water and Solutes in Plants 


""What else is the function of a forest, first and foremost, if not a place to 
do this: to capture and filter water and merge with sunlight, to create 
intricate being, intricate matter?"" Rick Bass, "The Larch", Orion 
Magazine, September/October 2012 


"The ability of trees to suck water from roots to leaves, sometimes to 
heights of over a hundred meters, is remarkable given the absence of any 
mechanical pump" wrote Harvey R. Brown in a review article in Physics in 
Perspective in 2013. Scientists have discovered quite a lot about this 
remarkable process, but that makes it no less remarkable. The structure of 
plant roots, stems, and leaves facilitates the transport of water, nutrients, 
and photosynthates throughout the plant. The phloem and xylem are the 
main tissues responsible for this movement. Water potential, 
evapotranspiration, and stomatal regulation influence how water and 
nutrients are transported in plants. To understand how these processes work, 
we must first understand the energetics of water potential. 


Water Potential 


Plants are phenomenal hydraulic engineers. Using only the basic laws of 
physics and the simple manipulation of potential energy, plants can move 
water to the top of a 116-meter-tall tree ([link]a). Plants can also use 
hydraulics to generate enough force to split rocks and buckle sidewalks 
({link |b). Plants achieve this because of water potential. 


(b) 


With heights nearing 116 meters, (a) coast 
redwoods (Sequoia sempervirens) are the tallest 
trees in the world. Plant roots can easily generate 
enough force to (b) buckle and break concrete 
sidewalks, much to the dismay of homeowners and 
city maintenance departments. (credit a: 
modification of work by Bernt Rostad; credit b: 
modification of work by Pedestrians Educating 
Drivers on Safety, Inc.) 


Water potential is a measure of the potential energy in water. Plant 
physiologists are not interested in the energy in any one particular aqueous 
system, but are very interested in water movement between two systems. In 
practical terms, therefore, water potential is the difference in potential 
energy between a given water sample and pure water (at atmospheric 
pressure and ambient temperature). Water potential is expressed in units of 
pressure (pressure is a form of energy) called megapascals (MPa). The 
potential of pure water is, by convenience of definition, designated a value 
of zero (even though pure water contains plenty of potential energy, that 
energy is ignored). Water potential values for the water in a plant root, stem, 
or leaf are therefore expressed relative to pure HO. 


The water potential in plant solutions is influenced by solute concentration, 
pressure, gravity, and factors called matrix effects. “System” can refer to the 


water potential of the soil water, root water, stem water, leaf water or the 
water in the atmosphere: whichever aqueous system is under consideration. 
As the individual components change, they raise or lower the total water 
potential of a system. When this happens, water moves to equilibrate, 
moving from the system or compartment with a higher water potential to 
the system or compartment with a lower water potential. This brings the 
difference in water potential between the two systems back to zero. 
Therefore, for water to move through the plant from the soil to the air (a 
process called transpiration), the water potential of the soil water > root 
water > stem water > leaf water > atmosphere water. 


Water only moves in response to changes in water potential, not in response 
to the individual components. However, because the individual components 
influence the total water potential of the system, by manipulating the 
individual components solute concentration, a plant can control water 
movement. 


Solute Potential 


Solute potential, also called osmotic potential, is negative in a plant cell and 
zero in distilled water. Typical values for cell cytoplasm are —0.5 to —1.0 
MPa. Solutes reduce water potential (resulting in a negative water potential) 
by consuming some of the potential energy available in the water. The 
internal water potential of a plant cell is more negative than pure water 
because of the cytoplasm’s high solute content ({link]). Because of this 
difference in water potential water will move from the soil into a plant’s 
root cells via the process of osmosis. This is why solute potential is 
sometimes called osmotic potential. 


H,0 


Pure water 
Positive Negative 
pressure pressure 
H,0 H,0 H,0 
<< <—_ 
Solute 
~__ ~~ 
Adding solute to the Applying positive Applying negative 
right side lowers ., pressure to the left pressure to the left 
Causing water to side increases Wp, side lowers Wp, 
move to the right causing water to causing water to 
side of the tube. move to the right move to the left side 
side of the tube. of the tube. 


In this example with a semipermeable 
membrane between two aqueous systems, 
water will move from a region of higher to 
lower water potential until equilibrium is 

reached. Solutes (W,), pressure (P,), and 
gravity (‘Y,) influence total water potential 
for each side of the tube (Wotqy M82 He"), 
and therefore, the difference between Viotai 
on each side (AV). (,, , the potential due to 
interaction of water with solid substrates, is 
ignored in this example because glass is not 
especially hydrophilic). Water moves in 
response to the difference in water potential 
between two systems (the left and right sides 
of the tube). 


Pressure Potential 


Pressure potential, also called turgor potential, may be positive or negative 
({link]). Because pressure is an expression of energy, the higher the 
pressure, the more potential energy in a system, and vice versa. An example 
of the effect of turgor pressure is the wilting of leaves and their restoration 
after the plant has been watered ((link]). Water lost from the leaves via 
transpiration is restored by uptake via the roots. 


A plant can manipulate turgor pressure via its ability to manipulate solute 
concentration and by the process of osmosis. If a plant cell increases the 
cytoplasmic solute concentration water will move into the cell by osmosis. 
Turgor pressure is also under indirect plant control via the opening and 
closing of stomata. Stomatal openings allow water to evaporate from the 
leaf, reducing the water potential of the leaf and increasing it between the 
water in the leaf and the petiole, thereby allowing water to flow from the 
petiole into the leaf. 


(a) (b) 


When (a) total water potential (Wotai) is 
lower outside the cells than inside, water 
moves out of the cells and the plant wilts. 

When (b) the total water potential is higher 
outside the plant cells than inside, water 
moves into the cells, resulting in turgor 

pressure (‘¥,) and keeping the plant erect. 

(credit: modification of work by Victor M. 

Vicente Selvas) 


Gravity Potential 


Gravity potential is always negative to zero in a plant with no height. It 
always removes or consumes potential energy from the system. The force of 
gravity pulls water downwards to the soil, reducing the total amount of 
potential energy in the water in the plan. The taller the plant, the taller the 
water column, and the more influence gravity has. On a cellular scale and in 
short plants, this effect is negligible and easily ignored. However, over the 
height of a tall tree like a coast redwood, the gravitational pull of -O.1 MPa 
is equivalent to an extra 1 MPa of resistance that must be overcome for 
water to reach the leaves of the tallest trees. 


Matric Potential 


The binding of water to a matrix of surrounding substances always removes 
or consumes potential energy from the system. Matric potential is similar to 
solute potential because it involves tying up the energy in an aqueous 
system by forming hydrogen bonds between the water and some other 
component. Matric potential is always negative to zero. In a dry system, it 
can be as low as —2 MPa in a dry seed, and it is zero in a water-saturated 
system. 


Movement of Water and Minerals in the Xylem 


Solutes, pressure, gravity, and matric potential are all important for the 
transport of water in plants. Water moves from an area of higher total water 
potential (higher Gibbs free energy) to an area of lower total water 
potential. Gibbs free energy is the energy associated with a chemical 
reaction that can be used to do work. 


Transpiration is the loss of water from the plant through evaporation at the 
leaf surface. It is the main driver of water movement in the xylem. 


Transpiration is caused by the evaporation of water at the leaf—atmosphere 
interface; it creates negative pressure (tension) equivalent to —2 MPa at the 
leaf surface. This value varies greatly depending on the vapor pressure 
deficit, which can be negligible at high relative humidity and substantial at 
low relative humidity. Water from the roots is pulled up by this tension. At 
night, when stomata shut and transpiration stops, the water is held in the 
stem and leaf by the adhesion of water to the cell walls of the xylem vessels 
and tracheids, and the cohesion of water molecules to each other. This is 
called the cohesion—tension theory of sap ascent. 


Inside the leaf at the cellular level, water on the surface of mesophyll cells 
saturates the cellulose microfibrils of the primary cell wall. The leaf 
contains many large intercellular air spaces for the exchange of oxygen for 
carbon dioxide, which is required for photosynthesis. The wet cell wall is 
exposed to this leaf internal air space, and the water on the surface of the 
cells evaporates into the air spaces, decreasing the thin film on the surface 
of the mesophyll cells. This decrease creates a greater tension on the water 
in the mesophyll cells ({link]), thereby increasing the pull on the water in 
the xylem vessels. The xylem vessels and tracheids are structurally adapted 
to cope with large changes in pressure. Rings in the vessels maintain their 
tubular shape, much like the rings on a vacuum cleaner hose keep the hose 
open while it is under pressure. Small perforations between vessel elements 
reduce the number and size of gas bubbles that can form via a process 
called cavitation. The formation of gas bubbles in xylem interrupts the 
continuous stream of water from the base to the top of the plant, causing a 
break termed an embolism in the flow of xylem sap. The taller the tree, the 
greater the tension forces needed to pull water, and the more cavitation 
events. In larger trees, the resulting embolisms can plug xylem vessels, 
making them non-functional. 


60000 00 


Atmosphere: 
~-100 MPa 


Transpiration draws Low 


water from the leaf. 
Leaf at tip of tree: 
~-1.5 MPa 


Water potential gradient 


Cohesion and adhesion 
draw water up the xylem. 
Stem:~-0.6 MPa 


Root hairs 


Root cells: ~—0.2 MPa 


Soil particle 


Water molecule 
Xylem 


draws water into the root. 


The cohesion—tension theory of sap 
ascent is shown. Evaporation from the 
mesophyll cells produces a negative 
water potential gradient that causes 
water to move upwards from the roots 
through the xylem. 


Transpiration is a passive process, meaning that metabolic energy in the 
form of ATP is not required for water movement. The energy driving 
transpiration is the difference in energy between the water in the soil and 
the water in the atmosphere. However, transpiration is tightly controlled. 


Control of Transpiration 


The atmosphere to which the leaf is exposed drives transpiration, but also 
causes massive water loss from the plant. Up to 90 percent of the water 
taken up by roots may be lost through transpiration. 


Leaves are covered by a waxy cuticle on the outer surface that prevents the 
loss of water. Regulation of transpiration, therefore, is achieved primarily 
through the opening and closing of stomata on the leaf surface. Stomata are 
surrounded by two specialized cells called guard cells, which open and 
close in response to environmental cues such as light intensity and quality, 
leaf water status, and carbon dioxide concentrations. Stomata must open to 
allow air containing carbon dioxide and oxygen to diffuse into the leaf for 
photosynthesis and respiration. When stomata are open, however, water 
vapor is lost to the external environment, increasing the rate of 
transpiration. Therefore, plants must maintain a balance between efficient 
photosynthesis and water loss. 


Plants have evolved over time to adapt to their local environment and 
reduce transpiration (({link]). Desert plant (xerophytes) and plants that grow 
on other plants (epiphytes) have limited access to water. Such plants usually 
have a much thicker waxy cuticle than those growing in more moderate, 
well-watered environments (mesophytes). Aquatic plants (hydrophytes) 
also have their own set of anatomical and morphological leaf adaptations. 


(c) (d) 


Plants are suited to their local environment. 
(a) Xerophytes, like this prickly pear cactus 
(Opuntia sp.) and (b) epiphytes such as this 
tropical Aeschynanthus perrottetii have 
adapted to very limited water resources. The 
leaves of a prickly pear are modified into 
spines, which lowers the surface-to-volume 
ratio and reduces water loss. Photosynthesis 
takes place in the stem, which also stores 
water. (b) A. perottetii leaves have a waxy 
cuticle that prevents water loss. (c) 
Goldenrod (Solidago sp.) is a mesophyte, 
well suited for moderate environments. (d) 


Hydrophytes, like this fragrant water lily 
(Nymphaea odorata), are adapted to thrive 
in aquatic environments. (credit a: 
modification of work by Jon Sullivan; credit 
b: modification of work by L. 
Shyamal/Wikimedia Commons; credit c: 
modification of work by Huw Williams; 
credit d: modification of work by Jason 
Hollinger) 


Xerophytes and epiphytes often have a thick covering of trichomes or of 
stomata that are sunken below the leaf’s surface. Trichomes are specialized 
hair-like epidermal cells that secrete oils and substances. These adaptations 
impede air flow across the stomatal pore and reduce transpiration. Multiple 
epidermal layers are also commonly found in these types of plants. 


Transportation of Photosynthates in the Phloem 


Plants need an energy source to grow. In seeds and bulbs, food is stored in 
polymers (such as starch) that are converted by metabolic processes into 
sucrose for newly developing plants. Once green shoots and leaves are 
growing, plants are able to produce their own food by photosynthesizing. 
The products of photosynthesis are called photosynthates, which are usually 
in the form of simple sugars such as sucrose. 


Structures that produce photosynthates for the growing plant are referred to 
as sources. Sugars produced in sources, such as leaves, need to be delivered 
to growing parts of the plant via the phloem in a process called 
translocation. The points of sugar delivery, such as roots, young shoots, and 
developing seeds, are called sinks. Seeds, tubers, and bulbs can be either a 
source or a sink, depending on the plant’s stage of development and the 
season. 


The products from the source are usually moved (translocated) to the 
nearest sink through the phloem. For example, the highest leaves will send 


photosynthates upward to the growing shoot tip, whereas lower leaves will 
direct photosynthates downward to the roots. Intermediate leaves will send 
products in both directions, unlike the flow in the xylem, which is always 
unidirectional (soil to leaf to atmosphere). The pattern of photosynthate 
flow changes as the plant grows and develops. Photosynthates are directed 
primarily to the roots early on, to shoots and leaves during vegetative 
growth, and to seeds and fruits during reproductive development. They are 
also directed to tubers for storage. 


Pressure Flow Model: Transport from Source to Sink 


Photosynthates, such as sucrose, are produced in the mesophyll cells of 
photosynthesizing leaves. From there they are translocated through the 
phloem to where they are used or stored. Mesophyll cells are connected by 
cytoplasmic channels called plasmodesmata. Photosynthates move through 
these channels to reach phloem sieve-tube elements (STEs) in the vascular 
bundles. From the mesophyll cells, the photosynthates are loaded into the 
phloem STEs. The sucrose is actively transported against its concentration 
gradient (a process requiring ATP) into the phloem cells using the 
electrochemical potential of the proton gradient. This is coupled to the 
uptake of sucrose with a carrier protein called the sucrose-H* symporter. 


Phloem STEs have reduced cytoplasmic contents, and are connected by a 
sieve plate with pores that allow for pressure-driven bulk flow, or 
translocation, of phloem sap. Companion cells are associated with STEs. 
They assist with metabolic activities and produce energy for the STEs 
({link]). 


Sieve tube 
element 


Companion 
cell 
Lateral sieve 


area 


Sieve tube 
plate 


Phloem is comprised 
of cells called sieve- 
tube elements. Phloem 
sap travels through 
perforations called 
sieve tube plates. 
Neighboring 
companion cells carry 
out metabolic 
functions for the sieve- 
tube elements and 
provide them with 
energy. Lateral sieve 
areas connect the 
sieve-tube elements to 
the companion cells. 


Once in the phloem, the photosynthates are translocated to the closest sink. 
Phloem sap is an aqueous solution that contains up to 30 percent sugar, 
minerals, amino acids, and plant growth regulators. The high percentage of 
sugar Causes water to move by osmosis from the adjacent xylem into the 


phloem tubes, thereby increasing pressure. This increase in total water 
potential causes the bulk flow of phloem from source to sink ([link]). 
Sucrose concentration in the sink cells is lower than in the phloem STEs 
because the sink sucrose has been metabolized for growth, or converted to 
starch for storage or other polymers, such as cellulose, for structural 
integrity. Unloading at the sink end of the phloem tube occurs by either 
diffusion or active transport of sucrose molecules from an area of high 
concentration to one of low concentration. Water diffuses from the phloem 
by osmosis and is then transpired or recycled via the xylem back into the 
phloem sap. This concept of how photosynthates move from the source to 
the sink is called the pressure flow model. 


Companion 
cell 


Source cell 
(leaf) 


Sink cell 
(root) 


Sucrose is actively 
transported from source 
cells into companion 
cells and then into the 
sieve-tube elements. 
This reduces the water 


potential, which causes 
water to enter the 


phloem from the xylem. 
The resulting positive 
pressure forces the 
sucrose-water mixture 
down toward the roots, 
where sucrose is 
unloaded. Transpiration 
causes water to return to 
the leaves through the 
xylem vessels. 


Nutritional Requirements of Plants 


"T died as mineral and became a plant," "I died as plant and rose to animal," 
"I died as animal and became man." "Why should I fear? When was I less 
by dying?" Jalal ad-Din ar-Rumi, Sufi poet (1207-73) 


Rumi's musings on minerals and plants contain a kernel of truth. Minerals 
become incorporated into the plant body, and are critically important in 
plant function. Plants are unique organisms that can absorb nutrients and 
water through their root system, as well as carbon dioxide from the 
atmosphere. Soil quality and climate are the major determinants of plant 
distribution and growth. The combination of soil nutrients, water, and 
carbon dioxide, along with sunlight, allows plants to grow. 


The Chemical Composition of Plants 


Since plants require nutrients in the form of elements such as carbon and 
potassium, it is important to understand the chemical composition of plants. 
The majority of volume in a plant cell is water; it typically comprises 80 to 
90 percent of the plant’s total weight. Soil is the water source for land 
plants, and can be an abundant source of water, even if it appears dry. Plant 
roots absorb water from the soil through root hairs and transport it up to the 
leaves through the xylem. As water vapor is lost from the leaves, the 
process of transpiration and the polarity of water molecules (which enables 
them to form hydrogen bonds) draws more water from the roots up through 
the plant to the leaves ([link]). Plants need water to support cell structure, 
for metabolic functions, to carry nutrients, and for photosynthesis. 


Root hairs 


Water is absorbed through the 
root hairs and moves up the 
xylem to the leaves. 


Plant cells need essential substances, collectively called nutrients, to sustain 
life. Plant nutrients may be composed of either organic or inorganic 
compounds. An organic compound is a chemical compound that contains 
carbon, such as carbon dioxide obtained from the atmosphere. Carbon that 
was obtained from atmospheric CO, composes the majority of the dry mass 
within most plants. An inorganic compound does not contain carbon and 
is not part of, or produced by, a living organism. Inorganic substances, 
which form the majority of the soil solution, are commonly called minerals: 
those required by plants include nitrogen (N) and potassium (K) for 
structure and regulation. 


Essential Nutrients 


Plants require only light, water and about 20 elements to support all their 
biochemical needs: these 20 elements are called essential nutrients ([link]). 
For an element to be regarded as essential, three criteria are required: 1) a 


plant cannot complete its life cycle without the element; 2) no other element 
can perform the function of the element; and 3) the element is directly 


involved in plant nutrition. 


Essential Elements for Plant Growth 


Macronutrients 
Carbon (C) 
Hydrogen (H) 
Oxygen (O) 
Nitrogen (N) 
Phosphorus (P) 
Potassium (K) 
Calcium (Ca) 
Magnesium (Mg) 


Sulfur (S) 


Micronutrients 
Iron (Fe) 
Manganese (Mn) 
Boron (B) 
Molybdenum (Mo) 
Copper (Cu) 
Zinc (Zn) 
Chlorine (Cl) 
Nickel (Ni) 
Cobalt (Co) 
Sodium (S) 


Silicon (Si) 


Macronutrients and Micronutrients 


The essential elements can be divided into two groups: macronutrients and 
micronutrients. Nutrients that plants require in larger amounts are called 
macronutrients. About half of the essential elements are considered 
macronutrients: carbon, hydrogen, oxygen, nitrogen, phosphorus, 
potassium, calcium, magnesium and sulfur. The first of these 
macronutrients, carbon (C), is required to form carbohydrates, proteins, 
nucleic acids, and many other compounds; it is therefore present in all 
macromolecules. On average, the dry weight (excluding water) of a cell is 
50 percent carbon. As shown in [link], carbon is a key part of plant 
biomolecules. 


Cellulose fibers 


Cellulose structure 


Cellulose, the main structural component of the 
plant cell wall, makes up over thirty percent of 
plant matter. It is the most abundant organic 
compound on earth. Plants are able to make 
their own cellulose, but need carbon from the 
soil to do so. 


The next most abundant element in plant cells is nitrogen (N); it is part of 
proteins and nucleic acids. Nitrogen is also used in the synthesis of some 
vitamins. Hydrogen and oxygen are macronutrients that are part of many 
organic compounds, and also form water. Oxygen is necessary for cellular 
respiration; plants use oxygen to store energy in the form of ATP. 
Phosphorus (P), another macromolecule, is necessary to synthesize nucleic 
acids and phospholipids. As part of ATP, phosphorus enables food energy to 
be converted into chemical energy through oxidative phosphorylation. 
Likewise, light energy is converted into chemical energy during 
photophosphorylation in photosynthesis, and into chemical energy to be 
extracted during respiration. Sulfur is part of certain amino acids, such as 
cysteine and methionine, and is present in several coenzymes. Sulfur also 
plays a role in photosynthesis as part of the electron transport chain, where 
hydrogen gradients play a key role in the conversion of light energy into 
ATP. Potassium (K) is important because of its role in regulating stomatal 
opening and closing. As the openings for gas exchange, stomata help 
maintain a healthy water balance; a potassium ion pump supports this 
process. 


Magnesium (Mg) and calcium (Ca) are also important macronutrients. The 
role of calcium is twofold: to regulate nutrient transport, and to support 
many enzyme functions. Magnesium is important to the photosynthetic 
process. These minerals, along with the micronutrients, which are described 
below, also contribute to the plant’s ionic balance. 


In addition to macronutrients, organisms require various elements in small 
amounts. These micronutrients, or trace elements, are present in very 
small quantities. They include boron (B), chlorine (Cl), manganese (Mn), 
iron (Fe), zinc (Zn), copper (Cu), molybdenum (Mo), nickel (Ni), silicon 
(Si), and sodium (Na). 


Deficiencies in any of these nutrients—particularly the macronutrients— 
can adversely affect plant growth ([Llink]. Depending on the specific 
nutrient, a lack can cause stunted growth, slow growth, or chlorosis 
(yellowing of the leaves). Extreme deficiencies may result in leaves 
showing signs of cell death. 


Nutrient deficiency is evident in the symptoms 
these plants show. This (a) grape tomato suffers 
from blossom end rot caused by calcium 
deficiency. The yellowing in this (b) Frangula 
alnus results from magnesium deficiency. 
Inadequate magnesium also leads to (c) 
intervenal chlorosis, seen here in a sweetgum 
leaf. This (d) palm is affected by potassium 
deficiency. (credit c: modification of work by 
Jim Conrad; credit d: modification of work by 
Malcolm Manners) 


Nutritional Adaptations of Plants 
B 


Introduction 

"The fixation of atmospheric nitrogen is one of the great discoveries, 
awaiting the genius of chemists." Sir William Crookes Presidential Address 
to the British Association for the Advancement of Science, 1898 


Of course, plants discovered how to fix nitrogen (convert N> gas to a form 
that can be incorporated in biological molecules such as nucleic acids and 
proteins) a long time ago. Or rather, they recruited nitrogen-fixing bacteria 
into a mutualistic relationship, where the bacteria fix nitrogen and provide 
nitrogen-containing compounds to the plant in exchange for food and 
shelter. 


Plants may also enlist the help of other microbial partners in nutrient 
acquisition. Particular species of bacteria and fungi have evolved along with 
certain plants to create a mutualistic symbiotic relationship with roots. This 
improves the nutrition of both the plant and the microbe. The formation of 
bacteria-containing nodules on the roots for nitrogen fixation, or the 
association of mycorrhizal fungi with roots for enhanced nutrient and water 
uptake, can be considered among the nutritional adaptations of plants. 
However, these are not the only type of adaptations that we may find; many 
plants have other adaptations that allow them to thrive under specific 
conditions. 


Nitrogen Fixation: Root and Bacteria Interactions 


Nitrogen is an important macronutrient because it is part of nucleic acids 
and proteins. Atmospheric nitrogen, which is the diatomic molecule N» or 
dinitrogen, is the largest pool of nitrogen in terrestrial ecosystems. 

However, plants cannot take advantage of this nitrogen because they do not 
have the necessary enzymes to convert it into biologically useful forms. 
However, nitrogen can be “fixed,” which means that it can be converted to 
ammonia (NH3) through biological, physical, or chemical processes. As you 
have learned, biological nitrogen fixation is the conversion of atmospheric 
nitrogen (N>) into ammonia (NHs3), exclusively carried out by prokaryotes 


such as soil bacteria or cyanobacteria. Biological processes contribute 65 
percent of the nitrogen used in agriculture. 


(a) (b) (c) 


Some common edible legumes—like (a) peanuts, (b) 
beans, and (c) chickpeas—are able to interact 
symbiotically with soil bacteria that fix nitrogen. (credit 
a: modification of work by Jules Clancy; credit b: 
modification of work by USDA) 


Nitrogen-fixing soil bacteria, collectively called rhizobia, symbiotically 
interact with legume roots to form specialized structures called nodules, in 
which nitrogen fixation takes place. This process entails the reduction of 
atmospheric nitrogen to ammonia, by means of the enzyme nitrogenase. 
Therefore, using rhizobia is a natural and environmentally friendly way to 
fertilize plants, as opposed to chemical fertilization that uses a 
nonrenewable resource, such as natural gas. Through symbiotic nitrogen 
fixation, the plant benefits from using an endless source of nitrogen from 
the atmosphere. The process simultaneously contributes to soil fertility 
because the plant root system leaves behind some of the biologically 
available nitrogen. As in any symbiosis, both organisms benefit from the 
interaction: the plant obtains ammonia, and bacteria obtain carbon 
compounds generated through photosynthesis, as well as a protected niche 
in which to grow ((Link]). 


Rhizobia inside vesicles 


Nitrogen-fixing nodules 


Soybean roots contain (a) nitrogen-fixing nodules. 
Cells within the nodules are infected with 
Bradyrhyzobium japonicum, a rhizobia or “root- 
loving” bacterium. The bacteria are encased in (b) 
vesicles inside the cell, as can be seen in this 
transmission electron micrograph. (credit a: 
modification of work by USDA; credit b: 
modification of work by Louisa Howard, Dartmouth 
Electron Microscope Facility; scale-bar data from 
Matt Russell) 


Mycorrhizae: The Symbiotic Relationship between Fungi and 
Roots 


A nutrient depletion zone can develop when there is rapid soil solution 
uptake, low nutrient concentration, low diffusion rate, or low soil moisture. 
These conditions are very common; therefore, most plants rely on fungi to 
facilitate the uptake of minerals from the soil. Fungi form symbiotic 
associations called mycorrhizae with plant roots, in which the fungi actually 
are integrated into the physical structure of the root. The fungi colonize the 
living root tissue during active plant growth. 


Through mycorrhization, the plant obtains mainly phosphate and other 
minerals, such as zinc and copper, from the soil. The fungus obtains 
nutrients, such as sugars, from the plant root ({link]). Mycorrhizae help 


increase the surface area of the plant root system because hyphae, which are 
narrow, can spread beyond the nutrient depletion zone. Hyphae can grow 
into small soil pores that allow access to phosphorus that would otherwise 
be unavailable to the plant. The beneficial effect on the plant is best 
observed in poor soils. The benefit to fungi is that they can obtain up to 20 
percent of the total carbon accessed by plants. Mycorrhizae functions as a 
physical barrier to pathogens. It also provides an induction of generalized 
host defense mechanisms, and sometimes involves production of antibiotic 
compounds by the fungi. 


Root tips proliferate in the 
presence of mycorrhizal infection, 
which appears as off-white fuzz in 
this image. (credit: modification of 

work by Nilsson et al., BMC 
Bioinformatics 2005) 


There are two types of mycorrhizae: ectomycorrhizae and 
endomycorrhizae. Ectomycorrhizae form an extensive dense sheath around 
the roots, called a mantle. Hyphae from the fungi extend from the mantle 
into the soil, which increases the surface area for water and mineral 
absorption. This type of mycorrhizae is found in forest trees, especially 


conifers, birches, and oaks. Endomycorrhizae, also called arbuscular 
mycorrhizae, do not form a dense sheath over the root. Instead, the fungal 
mycelium is embedded within the root tissue. Endomycorrhizae are found 
in the roots of more than 80 percent of terrestrial plants. 


Nutrients from Other Sources 


Some plants cannot produce their own food and must obtain their nutrition 
from outside sources. This may occur with plants that are parasitic or 
saprophytic. Some plants are mutualistic symbionts, epiphytes, or 
insectivorous. 


Plant Parasites 


A parasitic plant depends on its host for survival. Some parasitic plants 
have no leaves. An example of this is the dodder ({link]), which has a weak, 
cylindrical stem that coils around the host and forms suckers. From these 
suckers, cells invade the host stem and grow to connect with the vascular 
bundles of the host. The parasitic plant obtains water and nutrients through 
these connections. The plant is a total parasite (a holoparasite) because it is 
completely dependent on its host. Other parasitic plants (hemiparasites) are 
fully photosynthetic and only use the host for water and minerals. There are 
about 4,100 species of parasitic plants. 


The dodder is a holoparasite that 
penetrates the host’s vascular 
tissue and diverts nutrients for its 
own growth. Note that the vines of 
the dodder, which has white 
flowers, are beige. The dodder has 
no chlorophyll and cannot produce 
its own food. (credit: 
"Lalithamba"/Flickr) 


Saprophytes 


A saprophyte is a plant that does not have chlorophyll and gets its food 
from dead matter, similar to bacteria and fungi (note that fungi are often 
called saprophytes, which is incorrect, because fungi are not plants). Plants 
like these use enzymes to convert organic food materials into simpler forms 
from which they can absorb nutrients ({link]). Most saprophytes do not 
directly digest dead matter: instead, they parasitize fungi that digest dead 
matter, or are mycorrhizal, ultimately obtaining photosynthate from a 
fungus that derived photosynthate from its host. Saprophytic plants are 
uncommon; only a few species are described. 


Saprophytes, like this Spotted Coralroot 
(Corallorhiza maculata), obtain their food 
from the mycelium of soil fungi, and do not 
have chlorophyll. The Spotted Coralroot is 
found in montane forests in northern and 
western North America and Central 
America. This specimen was photographed 
in the Pecos Wilderness area in New 
Mexico. (credit: photo by D. A. Rintoul) 


Epiphytes 


An epiphyte is a plant that grows on other plants, but is not dependent upon 
the other plant for nutrition ({link]). Epiphytes have two types of roots: 
clinging aerial roots, which absorb nutrients from humus that accumulates 


in the crevices of trees; and aerial roots, which absorb moisture from the 
atmosphere. 


These epiphyte plants 
grow in the main 
greenhouse of the Jardin 
des Plantes in Paris. 


Insectivorous Plants 


An insectivorous plant has specialized leaves to attract and digest insects. 
You are probably familiar with the Venus flytrap, which has leaves that 
work as snap-traps . Other kinds of carnivorous plants, such as the sundews, 
are decorated with glands that secrete a sticky fluid which both attracts and 
then later digests insects that become ensnared in the sticky fluid. And still 
another group includes the pitcher plants, which typically catch and hold 


rainwater in a pitcher-shaped organ. The plant secretes nutrients as well as 
digestive enzymes into the trapped water. Insects are attracted to, and then 
fall into, the pool of fluid; they cannot easily escape due to the downward- 
facing hairs that line the inside of the "pitcher". One unique kind of pitcher 
plant is the California Pitcher Plant (Darlingtonia californica, [link]), found 
in bogs and seeps in the mountains of northern California and southern 
Oregon. The plant, also known as the Cobra Lily, is unique in that it does 
not trap rainwater in the pitcher, but rather pumps it up from the roots. A 
tiny entrance hole underneath the "head" of the cobra-shaped structure 
allows insects in, but they cannot get back out once they are trapped in the 
digestive fluid stored below. All carnivorous plants are found in nitrogen- 
poor soils, and obtain the bulk of this critical nutrient from the bodies of 
insects and other animals that they trap and digest. 


A California Pitcher Plant has 
specialized leaves to trap insects. 
This specimen was photographed 
in the Trinity Alps Wilderness in 
northern California. (credit: photo 

by D. A. Rintoul) 


Photosynthetic Pathways 


"You can't have a light without a dark to stick it in"." Arlo Guthrie, American 
musician 


In a previous module, you learned about photosynthesis, the mechanism plants 
use to convert solar energy into chemical energy. The light energy captured is 
used to make ATP and NADPH, which is then used to reduce carbon from a 
simple form (CO >) into a more complex form (sugars). The first step of the 
Calvin cycle is the fixation of carbon dioxide to RuBP, and the plants that only 
use this mechanism of carbon fixation are called C3 plants. About 85% of the 
plant species on the planet are C3 plants; some examples are rice, wheat, 
soybeans and all trees. 


The process of photosynthesis has a theoretical efficiency of 30% (i.e., the 
maximum amount of chemical energy output would be only 30% of the solar 
energy input), but in reality the efficiency is much lower. It is only about 3% on 
cloudy days. Why is so much solar energy lost? There are a number of factors 
contributing to this energy loss, and one metabolic pathway that contributes to 
this low efficiency is photorespiration. During photorespiration, the key 
photosynthetic enzyme Rubisco (ribulose-1,5-bisphosphate carboxylase 
oxygenase) uses O, as a substrate instead of CO>. This process uses up a 
considerable amount of energy without making sugars ([link]). When a plant has 
its stomata open (CO; is diffusing in while O> and water are diffusing out), 
photorespiration is minimized because Rubisco has a higher affinity for CO 
than for O» when air temperatures are below 30°C (86°F). However, when a 
plant closes its stomata during times of water stress and O> from photosynthesis 
builds up inside the cell, the rate of photorespiration increases because O, is now 
more abundant inside the mesophyll. So, there is a tradeoff. Plants can leave the 
stomata open and risk drying out, or they can close the stomata, thereby reducing 
the uptake of CO», and decreasing the efficiency of photosynthesis. In addition, 
Rubisco has a higher affinity for O2 when temperatures increase, which means 
that C3 plants use more energy (ATP) for photorespiration at higher 
temperatures. 


ATP | co, O, ATP 


ATP PGA ATP 
NADPH NADPH 


A comparison of photorespiration and carbon fixation in C3 plants. 
During photorespiration, O» is bound to RuBP and forms 
phosphoglycolate (PG) and Phosphoglycerate (PGA), PG then 
undergoes an number energy requiring reactions releasing CO2. Work 
by Eva Horne. 


Evolutionarily speaking, why is photorespiration still around? One hypothesis is 
that it is evolutionary baggage from a time when the atmosphere had a lower O> 
concentration than it does today. In other words, when Rubisco first evolved 
millions of years ago, the O» concentration was so low that excluding O, from its 
binding site had little or no influence on the efficiency of photosynthesis. The 
modern Rubisco retains some of its ancestral affinity for O2, which leads to the 
energy costs associated with photorespiration. However, plant cell physiologists 
are discovering that there might be some metabolic benefits associated with 
photorespiration, which would help explain why this seemingly wasteful 
pathway is still found in plants. Adding to the dilemma is the fact that when 
plant geneticists “knock out” Rubisco’s ability to fix Oz, Rubisco also loses its 
ability to fix COs. It is possible that the active site of this enzyme cannot be 
engineered, by artificial or natural selection, so that it exclusively binds CO, and 
not Op. 


C, plant and CAM Pathways as a Means of Reducing 
Photorespiration 


The Cy and CAM pathways for fixing CO> are two adaptations that improve the 
efficiency of photosynthesis, by ensuring that Rubisco encounters high CO» 
concentrations and thus reduces photorespiration. These two photosynthetic 
adaptations for fixing CO» have evolved independently a number of times in 
species that evolved from wet and dry, but typically warm climates. Why have 
these mechanisms evolved independently so many times? Plants that minimize 
photorespiration may have a significant competitive advantage, because a 
considerable amount of energy (in the form of ATP) is lost in plants during 
photorespiration. In many environments, plants that use solar energy more 
efficiently should out-compete those which are less efficient. 


C, Pathway 


In Cy plants, the reactions that fix atmospheric CO, and the Calvin cycle are 
physically separated, with the reactions that fix atmospheric CO, occurring in 
the mesophyll cells and the Calvin cycle occurring in special cells that surround 
the veins in the leaves. These cells are called bundle-sheath cells. How does this 
work? Atmospheric CO; is fixed in the mesophyll cells as a simple 4-carbon 
organic acid (malate) by an enzyme that has no affinity for O». Malate is then 
transported to the bundle-sheath cells. Inside the bundle sheath, malate is 
oxidized to a 3-C organic acid, and in the process, 1 molecule of CO; is 
produced from every malate molecule ({link]). The CO, is then fixed by Rubisco 
into sugars, via the Calvin cycle, exactly as in C3 photosynthesis. There is an 
additional cost of two ATPs associated with moving the three-carbon “ferry” 
molecule from the bundle sheath cell back to the mesophyll to pick up another 
molecule of atmospheric CO>. Since the spatial separation in bundle-sheath cells 
minimizes O> concentrations in the locations where Rubisco is located, 
photorespiration is minimized ([link]). This arrangement of cells reduces 
photorespiration and increases the efficiency of photosynthesis for C, plants. In 
addition, Cy plants require about half as much water as a C3 plant. The reason Cy 
plants require less water is due to the fact that the physical shape of the stomata 
and leaf structure of C, plants helps reduce water loss by developing a large CO» 
concentration gradient between the outside of the leaf (400 ppm) and the 
mesophyll cells (10 ppm). The large CO» concentration gradient reduces water 
loss via transpiration through the stomata. 


C; plant C, plant 


Stoma Vascular Bundle Mesophyll 
tissue sheath cell 
cell 


Vascular Mesophyll 
tissue cell 


Stoma 


Bundle sheath cell 


Cross section of a C3 and Cy, plant leaf. Work by Eva Horne 


The spatial separation of Carbon 
fixation and the Calvin cycle in C, 
plants. Work by Eva Horne 


The C4 pathway is used in about 3% of all vascular plants; some examples are 
crabgrass, sugarcane and corn. Cy plants are common in habitats that are hot, but 
are less abundant in areas that are cooler, because the enzyme that fixes the CO, 
in the mesophyll is less efficient at lower temperature. One hypothesis for the 
abundance of Cy, plants in hot habitats is that the benefits of reduced 
photorespiration and water loss exceeds the ATP cost of moving the the CO) 
from the mesophyll cell to bundle-sheath cell. 


CAM 


Many plants such as cacti and pineapples, which are adapted to arid 
environments, use a different energy and water saving pathway called 
crassulacean acid metabolism (CAM). This name comes from the family of 
plants (Crassulaceae) in which scientists first discovered the pathway. Instead of 
separating the light-dependent reactions and the use of CO, in the Calvin cycle 
spatially, CAM plants separate these processes temporally ({link]). At night, 
CAM plants open their stomata, and an enzyme in the mesophyll cells fix the 
CO, as an organic acid and store the organic acid in vacuoles until moming. 
During the day the light-dependent reactions supply the ATP and NADPH 
necessary for the Calvin cycle to function, and the CO, is released from those 
organic acids and used to make sugars. Plant species using CAM photosynthesis 
are the most water efficient of all; the stomata are only open at night when 
humidity is typically higher and the temperatures are much cooler (which serves 
to lower the diffusive gradient driving water loss from leaves). The CAM 
pathway is primarily an adaptation to water-limited environments; the fact that 
this pathway also stops photorespiration is an added benefit. 


Temporal separation of Carbon 
fixation and the Calvin cycle in 
CAM plants. Work by Eva Horne 


Overall, C3, C4 and CAM plants all use the Calvin cycle to make sugars from 
CO>. However, the various ways in which plants fix CO, varies with the 
advantages and disadvantages associated with the mechanism and the habitats 
where plants can be found (Table 1). 


As humans continue to burn fossil fuels, CO, levels in the atmosphere will 
continue to increase. This human alteration of the environment has sparked the 
development of a number of interesting questions. What influence will 
increasing CO> have on the distributions of C3, C, and CAM plants? What 
influence will increasing CO, have on agricultural production? Is it possible that 
an increase in agricultural production by additional CO, in the atmosphere could 


offset or mitigate the decrease in agricultural production caused by climate 


change? 


Cost 


Benefits 


Separation 
of light- 
dependent 
reactions 
and 
carbon 
fixation 


Habitat 


C3 plant 


Photorespiration 


Carbon fixation 
without using 
ATP 


None, all of 
these reactions 
occur in the 
same cells 


Cool and moist 


C, plant 


ATP cost 
associated with 
fixing carbon 
twice. Carbon 
fixation is less 
efficient under 
cold conditions. 


Reduced 
photorespiration 
and ability to 
fix Carbon 
under high 
temperatures 
and reduced 
water loss 


Spatial, these 
two sets of 
reactions occur 
in different cells 


Hot, not in cold 
environments 
(see cost.) 


CAM Plant 


Reduced 
amount of fixed 
carbon, stomata 
only open at 
night 


Reduced 
photorespiration 
and reduced 
water loss 


Temporal, these 
two sets of 
reactions occur 
at different 
times of day 


Hot and dry, 
large 
temperature 
differential 


between night 
and day 


Characteristics of C3, Cz and CAM methods of fixing CO, 


Climate and the Effects of Global Climate Change 


""Every year, by burning fossil fuels, we release a million years of 
photosynthesis" Daniel Nocera, an MIT scientist working to develop a 
process which uses sunlight and water to produce energy, quoted in "The 
Artificial Leaf" by Daniel Owen, The New Yorker, May 14, 2012. 


All biomes are affected by global conditions, such as climate, that 
ultimately shape each biome’s environment. Scientists who study climate 
have noted a series of marked changes that have gradually become 
increasingly evident during the last sixty years. Global climate change is 
the term used to describe altered global weather patterns, including a 
worldwide increase in temperature, due largely to rising levels of 
atmospheric carbon dioxide. 


Climate and Weather 


A common misconception about global climate change is that a specific 
weather event occurring in a particular region (for example, a very cool 
week in June in central Indiana) is evidence of global climate change. 
However, a cold week in June is a weather-related event and not a climate- 
related one. These misconceptions often arise because of confusion over the 
terms climate and weather. 


Climate refers to the long-term, predictable atmospheric conditions of a 
specific area. The climate of a biome is characterized by having consistent 
temperature and annual rainfall ranges. Climate does not address the 
amount of rain that fell on one particular day in a biome or the colder-than- 
average temperatures that occurred on one day. In contrast, weather refers 
to the conditions of the atmosphere during a short period of time. Weather 
forecasts are usually made for 48-hour cycles. Long-range weather 
forecasts are available but can be unreliable. 


To better understand the difference between climate and weather, imagine 
that you are planning an outdoor event in northern Wisconsin. You would 
be thinking about climate when you plan the event in the summer rather 
than the winter because you have long-term knowledge that any given 


Saturday in the months of May to August would be a better choice for an 
outdoor event in Wisconsin than any given Saturday in January. However, 
you cannot determine the specific day that the event should be held on 
because it is difficult to accurately predict the weather on a specific day. 
Climate can be considered “average” weather. 


Global Climate Change 
Climate change can be understood by approaching three areas of study: 


¢ current and past global climate change 
¢ causes of past and present-day global climate change 
¢ ancient and current results of climate change 


It is helpful to keep these three different aspects of climate change clearly 
separated when consuming media reports about global climate change. It is 
common for reports and discussions about global climate change to confuse 
the data showing that Earth’s climate is changing with the factors that drive 
this climate change. 


Evidence for Global Climate Change 


Since scientists cannot go back in time to directly measure climatic 
variables, such as average temperature and precipitation, they must instead 
indirectly measure temperature. To do this, scientists rely on historical 
evidence of Earth’s past climate. 


Antarctic ice cores are a key example of such evidence. These ice cores are 
samples of polar ice obtained by means of drills that reach thousands of 
meters into ice sheets or high mountain glaciers. Viewing the ice cores is 
like traveling backwards through time; the deeper the sample, the earlier the 
time period. Trapped within the ice are bubbles of air and other biological 
evidence that can reveal temperature and carbon dioxide data. Antarctic ice 
cores have been collected and analyzed to indirectly estimate the 
temperature of the Earth over the past 400,000 years ([link]a). The 0 °C on 
this graph refers to the long-term average. Temperatures that are greater 


than 0 °C exceed Earth’s long-term average temperature. Conversely, 
temperatures that are less than 0 °C are less than Earth’s average 
temperature. This figure shows that there have been periodic cycles of 
increasing and decreasing temperature. 


Before the late 1800s, the Earth has been as much as 9 °C cooler and about 
3 °C warmer. Note that the graph in [link]b shows that the atmospheric 
concentration of carbon dioxide has also risen and fallen in periodic cycles; 
note the relationship between carbon dioxide concentration and 
temperature. [link ]b shows that carbon dioxide levels in the atmosphere 
have historically cycled between 180 and 300 parts per million (ppm) by 
volume. 


Ls] 
“i 
ua 


S 
a 


CO, concentration (ppm) 
N 
3 


8 


~~ 
ua 


Ice at the Russian Vostok station 
in East Antarctica was laid down 


over the course 420,000 years and 
reached a depth of over 3,000 m. 
By measuring the amount of CO» 
trapped in the ice, scientists have 
determined past atmospheric CO> 
concentrations. Temperatures 
relative to modern day were 
determined from the amount of 
deuterium (an isotope of 
hydrogen) present. 


[link]a does not show the last 2,000 years with enough detail to compare 
the changes of Earth’s temperature during the last 400,000 years with the 
temperature change that has occurred in the more recent past. Two 
significant temperature anomalies, or irregularities, have occurred in the last 
2000 years. These are the Medieval Climate Anomaly (or the Medieval 
Warm Period) and the Little Ice Age. A third temperature anomaly aligns 
with the Industrial Era. The Medieval Climate Anomaly occurred between 
900 and 1300 AD. During this time period, many climate scientists think 
that slightly warmer weather conditions prevailed in many parts of the 
world; the higher-than-average temperature changes varied between 0.10 °C 
and 0.20 °C above the norm. Although 0.10 °C does not seem large enough 
to produce any noticeable change, it did free seas of ice. Because of this 
warming, the Vikings were able to colonize Greenland. 


The Little Ice Age was a cold period that occurred between 1550 AD and 
1850 AD. During this time, a slight cooling of a little less than 1 °C was 
observed in North America, Europe, and possibly other areas of the Earth. 
This 1 °C change in global temperature is a seemingly small deviation in 
temperature (as was observed during the Medieval Climate Anomaly); 
however, it also resulted in noticeable changes. Historical accounts reveal a 
time of exceptionally harsh winters with much snow and frost. 


The Industrial Revolution, which began around 1750, was characterized by 
changes in much of human society. Advances in agriculture increased the 


food supply, which improved the standard of living for people in Europe 
and the United States. New technologies were invented and provided jobs 
and cheaper goods. These new technologies were powered using fossil 
fuels, especially coal. The Industrial Revolution starting in the early 
nineteenth century ushered in the beginning of the Industrial Era. When a 
fossil fuel is burned, carbon dioxide is released. With the beginning of the 
Industrial Era, atmospheric carbon dioxide began to rise ([link]). 


Atmospheric CO, at Mauna Loa Observatory 
400 


Scripps Institution of Oceanography 
NOAA Earth System Research Laboratory 


380 


360 


340 


PARTS PER MILLION 


320 


March 2014 


1960 1970 1980 1990 2000 2010 
YEAR 


The atmospheric concentration of CO, has risen steadily since the 
beginning of industrialization. Graph from 
http://www.esrl.noaa.gov/gmd/webdata/ccg¢g/trends/co2_data_mlo.pdf 


Current and Past Drivers of Global Climate Change 


Scientists also use indirect evidence to determine the drivers, or factors, that 
may be responsible for climate change. The indirect evidence includes data 
collected using ice cores, boreholes (a narrow shaft bored into the ground), 
tree rings, glacier lengths, pollen remains, and ocean sediments. The data 
shows a correlation between the timing of temperature changes and drivers 
of climate change: before the Industrial Era (pre-1780), there were three 
drivers of climate change that were not related to human activity or 
atmospheric gases. The first of these is the Milankovitch cycles. The 
Milankovitch cycles describe the effects of slight changes in the Earth’s 
orbit on Earth’s climate. The length of the Milankovitch cycles ranges 
between 19,000 and 100,000 years. In other words, one could expect to see 
some predictable changes in the Earth’s climate associated with changes in 
the Earth’s orbit at a minimum of every 19,000 years. 


The variation in the sun’s intensity is the second natural factor responsible 
for climate change. Solar intensity is the amount of solar power or energy 
the sun emits in a given amount of time. There is a direct relationship 
between solar intensity and temperature. As solar intensity increases (or 
decreases), the Earth’s temperature correspondingly increases (or 
decreases). Changes in solar intensity have been proposed as one of several 
possible explanations for the Little Ice Age. 


Finally, volcanic eruptions are a third natural driver of climate change. 
Volcanic eruptions can last a few days, but the solids and gases released 
during an eruption can influence the climate over a period of a few years, 
causing short-term climate changes. The gases and solids released by 
volcanic eruptions can include carbon dioxide, water vapor, sulfur dioxide, 
hydrogen sulfide, hydrogen, and carbon monoxide. Generally, volcanic 
eruptions cool the climate. This occurred in 1783 when volcanos in Iceland 
erupted and caused the release of large volumes of sulfuric oxide. This led 
to haze-effect cooling, a global phenomenon that occurs when dust, ash, or 
other suspended particles block out sunlight and trigger lower global 
temperatures as a result; haze-effect cooling usually extends for one or 
more years. In Europe and North America, haze-effect cooling produced 


some of the lowest average winter temperatures on record in 1783 and 
1784. 


Greenhouse gases are probably the most significant drivers of the climate. 
When heat energy from the sun strikes the Earth, gases known as 
greenhouse gases trap the heat in the atmosphere, as do the glass panes of a 
greenhouse keep heat from escaping. The greenhouse gases that affect Earth 
include carbon dioxide, methane, water vapor, nitrous oxide, and ozone. 
Approximately half of the radiation from the sun passes through these gases 
in the atmosphere and strikes the Earth. This radiation is converted into 
thermal radiation on the Earth’s surface, and then a portion of that energy is 
re-radiated back into the atmosphere. Greenhouse gases, however, reflect 
much of the thermal energy back to the Earth’s surface. The more 
greenhouse gases there are in the atmosphere, the more thermal energy is 
reflected back to the Earth’s surface. Greenhouse gases absorb and emit 
radiation and are an important factor in the greenhouse effect: the warming 
of Earth due to carbon dioxide and other greenhouse gases in the 
atmosphere. 


Evidence supports the relationship between atmospheric concentrations of 
carbon dioxide and temperature: as carbon dioxide rises, global temperature 
rises. Since 1950, the concentration of atmospheric carbon dioxide has 
increased from about 280 ppm to 382 ppm in 2006. In 2013, the 
atmospheric carbon dioxide concentration was 400 ppm. 


Scientists look at patterns in data and try to explain differences or 
deviations from these patterns. The atmospheric carbon dioxide data reveal 
a historical pattern of carbon dioxide increasing and decreasing, cycling 
between a low of 180 ppm and a high of 300 ppm. Scientists have 
concluded that it took around 50,000 years for the atmospheric carbon 
dioxide level to increase from its low minimum concentration to its higher 
maximum concentration. However, starting recently, atmospheric carbon 
dioxide concentrations have increased beyond the historical maximum of 
300 ppm. The current increases in atmospheric carbon dioxide have 
happened very quickly—in a matter of hundreds of years rather than 
thousands of years. What is the reason for this difference in the rate of 
change and the amount of increase in carbon dioxide? A key factor that 


must be recognized when comparing the historical data and the current data 
is the presence of modern human society; no other driver of climate change 
has yielded changes in atmospheric carbon dioxide levels at this rate or to 
this magnitude. 


Human activity releases carbon dioxide and methane, two of the most 
important greenhouse gases, into the atmosphere in several ways. The 
primary mechanism that releases carbon dioxide is the burning of fossil 
fuels, such as gasoline, coal, and natural gas ([{link]). Deforestation, cement 
manufacture, animal agriculture, the clearing of land, and the burning of 
forests are other human activities that release carbon dioxide. Methane 
(CH,) is produced when bacteria break down organic matter under 
anaerobic conditions. Anaerobic conditions can happen when organic 
matter is trapped underwater (such as in rice paddies) or in the intestines of 
herbivores. Methane can also be released from natural gas fields and the 
decomposition that occurs in landfills. Another source of methane is the 
melting of clathrates. Clathrates are frozen chunks of ice and methane 
found at the bottom of the ocean. When water warms, these chunks of ice 
melt and methane is released. As the ocean’s water temperature increases, 
the rate at which clathrates melt is increasing, releasing even more methane. 
This leads to increased levels of methane in the atmosphere, which further 
accelerates the rate of global warming. This is an example of the positive 
feedback loop that is leading to the rapid rate of increase of global 
temperatures. 


The burning of fossil 
fuels in industry and by 
vehicles releases carbon 

dioxide and other 
greenhouse gases into the 
atmosphere. (credit: 
“P6oll6”/Wikimedia 


Commons) 


Documented Results of Climate Change: Past and Present 


Scientists have geological evidence of the consequences of long-ago 
climate change. Modern-day phenomena such as retreating glaciers and 
melting polar ice cause a continual rise in sea level. Meanwhile, changes in 
climate can negatively affect organisms. 


Past Climate Change 


Global warming has been associated with at least one planet-wide 
extinction event during the geological past. The Permian extinction event 
occurred about 251 million years ago toward the end of the roughly 50- 
million-year-long geological time span known as the Permian period. This 
geologic time period was one of the three warmest periods in Earth’s 
geologic history. Scientists estimate that approximately 70 percent of the 
terrestrial plant and animal species and 84 percent of marine species 
became extinct, vanishing forever near the end of the Permian period. 
Organisms that had adapted to wet and warm climatic conditions, such as 
annual rainfall of 300-400 cm (118-157 in) and 20 °C—30 °C (68 °F-86 °F) 
in the tropical wet forest, may not have been able to survive the Permian 
climate change. 


Present Climate Change 


A number of global events have occurred that may be attributed to climate 
change during our lifetimes. Glacier National Park in Montana is 
undergoing the retreat of many of its glaciers, a phenomenon known as 
glacier recession. In 1850, the area contained approximately 150 glaciers. 
By 2010, however, the park contained only about 24 glaciers greater than 
25 acres in size. One of these glaciers is the Grinnell Glacier ({link]) at 
Mount Gould. Between 1966 and 2005, the size of Grinnell Glacier shrank 
by 40 percent. Similarly, the mass of the ice sheets in Greenland and the 
Antarctic is decreasing: Greenland lost 150-250 km? of ice per year 
between 2002 and 2006. In addition, the size and thickness of the Arctic sea 
ice is decreasing. 


The effect of global warming can be seen in the continuing 
retreat of Grinnel Glacier. The mean annual temperature in the 
park has increased 1.33 °C since 1900. The loss of a glacier 
results in the loss of summer meltwaters, sharply reducing 
seasonal water supplies and severely affecting local 
ecosystems. (credit: modification of work by USGS) 


This loss of ice is leading to increases in the global sea level. On average, 
the sea is rising at a rate of 1.8 mm per year. However, between 1993 and 
2010 the rate of sea level increase ranged between 2.9 and 3.4 mm per year. 
A variety of factors affect the volume of water in the ocean, including the 
temperature of the water (the density of water is related to its temperature) 
and the amount of water found in rivers, lakes, glaciers, polar ice caps, and 
sea ice. As glaciers and polar ice caps melt, there is a significant 
contribution of liquid water that was previously frozen. 


In addition to some abiotic conditions changing in response to climate 
change, many organisms are also being affected by the changes in 
temperature. Temperature and precipitation play key roles in determining 
the geographic distribution and phenology of plants and animals. 
(Phenology is the study of the effects of climatic conditions on the timing of 
periodic lifecycle events, such as flowering in plants or migration in birds.) 
Researchers have shown that 385 plant species in Great Britain are 
flowering 4.5 days sooner than was recorded earlier during the previous 40 
years. In addition, insect-pollinated species were more likely to flower 


earlier than wind-pollinated species. The impact of changes in flowering 
date would be mitigated if the insect pollinators emerged earlier. This 
mismatched timing of plants and pollinators could result in injurious 
ecosystem effects because, for continued survival, insect-pollinated plants 
must flower when their pollinators are present. 


Human Population Continues to Grow 


Introduction 

"Population, when unchecked, increases in a geometrical ratio. Subsistence 
increases only in an arithmetical ratio. A slight acquaintance with numbers 
will show the immensity of the first power in comparison of the second." 
Thomas Robert Malthus. An Essay on the Principle of Population, (1798) 


Mathematical approaches to understanding animal population dynamics, 
which you learned about earlier in the semester, can be applied to human 
population growth. Malthus recognized long ago that exponential 
population growth might be a problem if resources increase non- 
exponentially. Resources can be increased by technology and other 
modifications to the environment. In fact, humans are not unique in their 
ability to alter their environment. For example, beaver dams alter the stream 
environment where they are built. Humans, however, have the ability to 
alter their environment to increase its carrying capacity sometimes to the 
detriment of other species (e.g., via artificial selection for crops that have a 
higher yield). Earth’s human population is growing rapidly, to the extent 
that some worry about the ability of the earth’s environment to sustain this 
population, as long-term exponential growth carries the potential risks of 
famine, disease, and large-scale death. 


Although humans have increased the carrying capacity of their 
environment, the technologies used to achieve this transformation have 
caused unprecedented changes to Earth’s environment, altering ecosystems 
to the point where some may be in danger of collapse. The depletion of the 
ozone layer, erosion due to acid rain, and damage from global climate 
change are caused by human activities. The ultimate effect of these changes 
on our carrying capacity is unknown. As some point out, it is likely that the 
negative effects of increasing carrying capacity will outweigh the positive 
ones—the carrying capacity of the world for human beings might actually 
decrease. 


The world’s human population is currently experiencing exponential growth 
even though human reproduction is far below its biotic potential ((link]). To 
reach its biotic potential, all females would have to become pregnant every 
nine months or so during their reproductive years. Also, resources would 


have to be such that the environment would support such growth. Neither of 
these two conditions exists. In spite of this fact, human population is still 
growing exponentially. 


— World 
== Africa 
_ == Asia 
~~ Europe 
3,000,000 = Latin America 
== Northern America 


5,000,000 


- 
(2) 
cs 
c 
cs 
wn 
s 
fo} 
£ 
2 
c 
7 
& 
2 
FE: 
= 
a 
fo} 
Qa 
cs 
~) 
o 
E 
E 
Ww 
Ww 


Human population growth since 1000 AD is 
exponential (dark blue line). Notice that while 
the population in Asia (yellow line), which has 
many economically underdeveloped countries, 

is increasing exponentially, the population in 

Europe (light blue line), where most of the 
countries are economically developed, is 
growing much more slowly. 


A consequence of exponential human population growth is the time that it 
takes to add a particular number of humans to the Earth is becoming 
shorter. [link] shows that 123 years were necessary to add 1 billion humans 
in 1930, but it only took 24 years to add two billion people between 1975 
and 1999. As already discussed, at some point it would appear that our 
ability to increase our carrying capacity indefinitely on a finite world is 
uncertain. Without new technological advances, the human growth rate has 
been predicted to slow in the coming decades. However, the population will 
still be increasing and the threat of overpopulation remains. 


Time between Billions in World Population Growth 


1 billion: 1800 
2 billion: 1930 
3 billion: 1960 
4 billion: 1975 
5 billion: 1987 
6 billion: 1999 
7 billion: 2012 
8 billion: 2028 
9 billion: 2054 


Years 


Source: Population Reference Bureau 


The time between the addition of each billion human 
beings to Earth decreases over time. (credit: 
modification of work by Ryan T. Cragun) 


Overcoming Density-Dependent Regulation 


Humans are unique in their ability to alter their environment with the 
conscious purpose of increasing its carrying capacity. This ability is a major 
factor responsible for human population growth and a way of overcoming 
density-dependent growth regulation. Much of this ability is related to 
human intelligence, society, and communication. Humans can construct 
shelter to protect them from the elements and have developed agriculture 
and domesticated animals to increase their food supplies. In addition, 
humans use language to communicate this technology to new generations, 
allowing them to improve upon previous accomplishments. 


Other factors in human population growth are migration and public health. 
Humans originated in Africa, but have since migrated to nearly all 
inhabitable land on the Earth. Public health, sanitation, and the use of 
antibiotics and vaccines have decreased the ability of infectious disease to 
limit human population growth. In the past, diseases such as the bubonic 


plaque of the fourteenth century killed between 30 and 60 percent of 
Europe’s population and reduced the overall world population by as many 
as 100 million people. Today, the threat of infectious disease, while not 
gone, is certainly less severe. According to the World Health Organization, 
global death from infectious disease declined from 14.2 million in 2000 to 
9.9 million in 2011. To compare to some of the epidemics of the past, the 
percentage of the world's population killed between 1993 and 2002 
decreased from 0.30 percent of the world's population to 0.24 percent. Thus, 
it appears that the influence of infectious disease on human population 
growth is becoming less significant. 


Long-Term Consequences of Exponential Human Population 
Growth 


Many dire predictions have been made about the world’s population leading 
to a major crisis called the “population explosion.” In the 1968 book The 
Population Bomb, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed 
all of humanity is over. In the 1970s hundreds of millions of people will 
Starve to death in spite of any crash programs embarked upon now. At this 
late date nothing can prevent a substantial increase in the world death 

rate,” footnote] While many critics view this statement as an exaggeration, the 
laws of exponential population growth are still in effect, and unchecked 
human population growth cannot continue indefinitely. 

Paul R. Erlich, prologue to The Population Bomb, (1968; repr., New York: 
Ballantine, 1970). 


Efforts to control population growth led to the one-child policy in China, 
which used to include more severe consequences, but now imposes fines on 
urban couples who have more than one child. Due to the fact that some 
couples wish to have a male heir, many Chinese couples continue to have 
more than one child. The policy itself, its social impacts, and the 
effectiveness of limiting overall population growth are controversial. In 
spite of population control policies, the human population continues to 
grow. At some point the food supply may run out because of the subsequent 
need to produce more and more food to feed our population. The United 
Nations estimates that future world population growth may vary from 6 
billion (a decrease) to 16 billion people by the year 2100. There is no way 


to know whether human population growth will moderate to the point 
where the crisis described by Dr. Ehrlich will be averted. 


Another result of population growth is the endangerment of the natural 
environment. Many countries have attempted to reduce the human impact 
on climate change by reducing their emission of the greenhouse gas carbon 
dioxide. However, these treaties have not been ratified by every country, 
and many underdeveloped countries trying to improve their economic 
condition may be less likely to agree with such provisions if it means 
slower economic development. Furthermore, the role of human activity in 
causing climate change has become a hotly debated socio-political issue in 
some developed countries, including the United States. Thus, we enter the 
future with considerable uncertainty about our ability to curb human 
population growth and protect our environment. 


Features of the Animal Kingdom 


Introduction 
"Stones grow; plants grow and live; animals grow, live and feel." Linneaus, 
in Philosophia Botanica, 1751 


The differences between the animal, vegetable and mineral classes are a bit 
more complicated than the simple scheme of Linneaus. Members of the 
animal kingdom are incredibly diverse, but all animals share common 
features that distinguish them from organisms in other kingdoms. All 
animals are eukaryotic, multicellular organisms, and almost all animals 
have specialized tissues. All animals are motile, at least during certain life 
stages. Animals require a source of food to grow and develop. All animals 
are heterotrophic, ingesting living or dead organic matter. This form of 
obtaining energy distinguishes them from autotrophic organisms, such as 
most plants, which make their own nutrients through photosynthesis and 
from fungi that digest their food externally. Animals may be carnivores, 
herbivores, omnivores, or parasites ([link]). Most animals reproduce 
sexually: The offspring pass through a series of developmental stages that 
establish a determined body plan, unlike plants, for example, in which the 
exact shape of the body is indeterminate. The body plan refers to the shape 
of an animal. 


(a) 


All animals that derive energy from food are heterotrophs. The 
(a) black bear is an omnivore, eating both plants and animals. 
The (b) heartworm Dirofilaria immitis is a parasite that derives 


energy from its hosts. It spends its larval stage in mosquitos 
and its adult stage infesting the hearts of dogs and other 
mammals, as shown here. (credit a: modification of work by 
USDA Forest Service; credit b: modification of work by Clyde 
Robinson) 


Complex Tissue Structure 


A hallmark trait of animals is specialized structures that are differentiated to 
perform unique functions. As multicellular organisms, most animals 
develop specialized cells that group together into tissues with specialized 
functions. A tissue is a collection of similar cells that had a common 
embryonic origin that share a specialized function. There are four main 
types of animal tissues: nervous, muscle, connective, and epithelial. 


e Nervous tissue contains neurons, or nerve cells, which transmit nerve 
impulses. 

e Muscle tissue contracts to cause all types of body movement from 
locomotion of the organism to movements within the body itself. You 
will learn more about the diferent types of muscle tissue later in this 
unit. 

e Animals also have specialized connective tissues that provide many 
functions, including transport and structural support. Examples of 
connective tissues include blood and bone. Connective tissue is 
comprised of cells separated by extracellular material made of organic 
and inorganic materials, such as the protein and mineral deposits of 
bone. 

e Epithelial tissue covers the internal and external surfaces of organs 
inside the animal body and the external surface of the body of the 
organism. 


Animal Reproduction and Development 


Most animals have diploid body (somatic) cells and a small number of 
haploid reproductive (gamete) cells produced through meiosis. Some 
exceptions exist: For example, in bees, wasps, and ants, the male is haploid 
because it develops from an unfertilized egg. Most animals undergo sexual 
reproduction, while many also have mechanisms of asexual reproduction. 


Asexual Reproduction 


Asexual reproduction, unlike sexual reproduction, produces offspring 
genetically identical to each other and to the parent. A number of animal 
species—especially those without backbones, but even some fish, 
amphibians, and reptiles—are capable of asexual reproduction. Asexual 
reproduction, except for occasional identical twinning, is absent in birds 
and mammals. The most common forms of asexual reproduction for 
stationary aquatic animals include budding and fragmentation, in which part 
of a parent individual can separate and grow into a new individual. In 
contrast, a form of asexual reproduction found in certain invertebrates and 
rare vertebrates is called parthenogenesis (or “virgin beginning”), in which 
unfertilized eggs develop into new offspring. 


Sexual Reproduction and Embryonic Development 


Almost all animal species are capable of reproducing sexually; for many, 
this is the only mode of reproduction possible. This distinguishes animals 
from fungi, protists, and bacteria, where asexual reproduction is common or 
exclusive. During sexual reproduction, the male and female gametes of a 
species combine in a process called fertilization. Typically, the small, motile 
male sperm travels to the much larger, sessile female egg. Sperm form is 
diverse and includes cells with flagella or amoeboid cells to facilitate 
motility. Fertilization and fusion of the gamete nuclei produce a zygote. 
Fertilization may be internal, especially in land animals, or external, as is 
common in many aquatic species. 


After fertilization, a developmental sequence ensues as cells divide and 
differentiate. Many of the events in development are shared in groups of 
related animal species, and these events are one of the main ways scientists 
classify high-level groups of animals. During development, animal cells 
specialize and form tissues, determining their future morphology and 
physiology. In many animals, such as mammals, the young resemble the 
adult. Other animals, such as some insects and amphibians, undergo 
complete metamorphosis in which individuals enter one or more larval 
stages. For these animals, the young and the adult have different diets and 
sometimes habitats. In other species, a process of incomplete 
metamorphosis occurs in which the young somewhat resemble the adults 
and go through a series of stages separated by molts (shedding of the skin) 
until they reach the final adult form. 


Features used in the Classification of Animals 


Animals are classified according to morphological and developmental 
characteristics, such as a body plan. With the exception of sponges, the 
animal body plan is symmetrical. This means that their distribution of body 
parts is balanced along an axis. Additional characteristics that contribute to 
animal classification include the number of tissue layers formed during 
development, the presence or absence of an internal body cavity, and other 
features of embryological development. 


Arthropods 


Ecdysozoa 


Protostomia 


Bilateria 
(bilateral 
symmetry, 
triploblastic) 


Eumetazoa 


(specialized 
tissues) 


Lophotrochozoa 


Metazoa Deuterostomia 
(animals) 


Radiata 
(radial symmetry, diploblastic) 


Parazoa (no tissues) 


The phylogenetic tree of animals is based on 
morphological, fossil, and genetic evidence. 


Body Symmetry 


Animals may be asymmetrical, radial, or bilateral in form ([link]). 
Asymmetrical animals are animals with no pattern or symmetry; an 
example of an asymmetrical animal is a sponge ([link]a). An organism with 
radial symmetry ((link]b) has a longitudinal (up-and-down) orientation: 
Any plane cut along this up—down axis produces roughly mirror-image 
halves. An example of an organism with radial symmetry is a sea anemone. 


Dorsal = 


| Posterior 


Asymmetry Radial symmetry Bilateral symmetry 
(a) (b) (c) 


Animals exhibit different types of body symmetry. The (a) 
sponge is asymmetrical and has no planes of symmetry, the (b) 
sea anemone has radial symmetry with multiple planes of 
symmetry, and the (c) goat has bilateral symmetry with one 
plane of symmetry. 


Bilateral symmetry is illustrated in [link]c using a goat. The goat also has 
upper and lower sides to it, but they are not symmetrical. A vertical plane 
cut from front to back separates the animal into roughly mirror-image right 
and left sides. Animals with bilateral symmetry also have a “head” and 
“tail” (anterior versus posterior) and a back and underside (dorsal versus 
ventral). 


Getting a Head 

A product of bilateral symmetry and of organisms having a head (anterior) 
and a tail (posterior) is the fact organisms move through their environment 
head first. Since organisms move through their environment head first, a 
significant advantage can be seen with organisms that have a concentration 
of sensory organs in the head region or cephalization. In other words, 
placement of sensory organs around the mouth of a heterotroph allows it to 
be more efficient at finding food. In addition, organisms moving around 
with the sensory organs in the front will be more efficient at detecting 
potential predators and not becoming food. 


Segmentation 


The division of an animal into repeating body parts is called segmentation. 
You can clearly see segmentation in earthworms and millipeds, but in some 
insects and chordates the subdivisions are not as obvious. What are the 
advantages of a segmented body? Segmentation allows for greater 
flexibility and mobility. The repeating body parts allows for specialization 
of specific body parts, such as the development of legs, arm and wings. 


Germ Layers 


Nearly all animal species undergo a layering of early tissues during 
embryonic development. These layers are called germ layers. Each layer 
develops into a specific set of tissues and organs. Animals develop either 
two or three embryonic germ layers ({link]). The animals that display radial 
symmetry develop two germ layers, an inner layer (endoderm) and an outer 
layer (ectoderm). These animals are called diploblasts. Animals with 
bilateral symmetry develop three germ layers: an inner layer (endoderm), an 
outer layer (ectoderm), and a middle layer (mesoderm). Animals with three 
germ layers are called triploblasts. 


Diploblast Triploblast 
Endoderm 


Digestive 
Cavity 


f+ Ectoderm 
Non-living layer Mesoderm 


During embryogenesis, diploblasts 
develop two embryonic germ layers: an 
ectoderm and an endoderm. Triploblasts 


develop a third layer—the mesoderm— 
between the endoderm and ectoderm. 


In triploblasts, the three germ layers develop in all the parts of an adult 


animal. The endoderm gives rise to the innermost lining of internal organs, 


such as those in the digestive tract, the liver, the pancreas and the lining of 
the lungs. The majority of organs and tissues in an adult animal such as the 
kidney, heart, muscles, blood vessels, bones and the dermis (inner layer of 
skin) develop from the mesoderm. Lastly, the ectoderm develops into the 
outermost layer of skin (epidermis), the lens and cornea of the eye, and the 
nervous system (brain and nerves). 


Germ 


Layer 


Ectoderm 


Mesoderm 


Endoderm 


Tissue types 


Outer layer of skin, nerves, brain, cornea and lens of 
the eye 


Connective tissue of skin (dermis), bone, muscle 
(including cardiac muscle), cartilage, blood cells and 
blood vessels, fat cells, reproductive tract 


Internal lining of organs of the digestive tract, internal 
lining of respiratory tract, liver 


Examples of tissue types that come from the three germ layers 


Presence or Absence of a Coelom 


Triploblasts may develop an internal body cavity lined with cells derived 
from mesoderm, called a coelom (pr. see-LOM). This epithelial-lined cavity 
is a space, usually filled with fluid, which lies between the digestive system 
and the body wall. It houses organs such as the kidneys and spleen, and 
contains the circulatory system. An Organ is a differentiated structure that 
performs a specific function in an organism; it consists of many cells and of 
various tissue types. Triploblasts that do not develop a coelom are called 
acoelomates, and this internal region is completely filled with tissue, 
although they have a gut cavity. Examples of acoelomates include the 
flatworms. Animals with a true coelom are called eucoelomates (or 
coelomates) ([link]). A true coelom arises entirely within the mesoderm 
germ layer. Animals such as earthworms, snails, insects, starfish, and 
vertebrates are all eucoelomates. A third group of triploblasts has a body 
cavity that is derived partly from mesoderm and partly from endoderm 
tissue. These animals are called pseudocoelomates. Roundworms are 
examples of pseudocoelomates. New data on the relationships of 
pseudocoelomates suggest that these phyla are not closely related and so the 
evolution of the pseudocoelom must have occurred more than once ([link]). 
True coelomates can be further characterized based on features of their 
early embryological development. 


Flatworm: Pseudobiceros bedfordi Annelid: Glycera Nematode: Heterodera glycines 


Pseudocoelom 
Digestive cavity 


Ectoderm 


Coelom 


Mesoderm 
Endoderm 


Mesoderm 


Digestive cavity Endoderm Ectoderm 


(a) Acoelomate (b) Eucoelomate (c) Pseudocoelomate 
(flatworms) (annelids, (roundworms) 
mollusks, 
arthropods, 


echinoderms, 
chordates) 


Triploblasts may be acoelomates, eucoelomates, or 
pseudocoelomates. Eucoelomates have a body cavity within the 
mesoderm, called a coelom, which is lined with mesoderm 
tissue. Pseudocoelomates have a similar body cavity, but it is 
lined with mesoderm and endoderm tissue. (credit a: 
modification of work by Jan Derk; credit b: modification of 
work by NOAA; credit c: modification of work by USDA, 
ARS) 


Protostomes and Deuterostomes 


Bilaterally symmetrical, triploblastic eucoelomates can be divided into two 
groups based on differences in their early embryonic development. You 
may have noticed in [link] the terms "Protostomia" and "Deuterostomia". 
Protostomes (members of the Protostomia) include phyla such as 
arthropods, mollusks, and annelids. Deuterostomes (members of the 


Deuterostomia) include the chordates and echinoderms. These two groups 
are named from which opening of the digestive cavity develops first: mouth 
or anus. The word protostome comes from Greek words meaning “mouth 
first,” and deuterostome originates from words meaning “mouth second” (in 
this case, the anus develops first). This difference reflects the fate of a 
structure called the blastopore ({link]), which becomes the mouth in 
protostomes and the anus in deuterostomes. There are other developmental 
differences between protostomes and deuterostomes, including the mode of 
formation of the coelom and the pattern of early cell division of the embryo. 


Protostomes Deuterostomes 


G 


Blastopore 
Coelom 


I Developing 


Mesoderm 
Mouth coelom 
Anus 


Digestive 
tube 


Anus Mouth 


Eucoelomates can be divided into two 
groups, protostomes and 
deuterostomes, based on their early 
embryonic development. Two of these 
differences include the origin of the 
mouth opening and the way in which 
the coelom is formed. 


Animal Tissue Types 


Introduction 

" The elementary parts of all tissues are formed of cells in an analogous, 
though very diversified manner, so that it may be asserted, that there is one 
universal principle of development for the elementary parts of organisms, 
however different, and that this principle is the formation of cells." Theodor 
Schwann, in Microscopic Researches into the Accordance in the Structure 
and Growth of Animals and Plants, 1839 


Cells make tissues, tissues make organs, and organs make organ systems. 
The tissues of multicellular, complex animals are four primary types: 
epithelial, connective, muscle, and nervous. Recall that tissues are groups of 
similar cells carrying out a specific related functions. Many different tissues 
combine to form an organ—like the skin or kidney—that have specialized 
functions within the body. Organs are organized into organ systems to 
perform functions; examples include the circulatory system, which consists 
of the heart and blood vessels, and the digestive system, consisting of 
several organs, including the stomach, intestines, liver, and pancreas. Organ 
systems come together to create an entire organism. 


Epithelial Tissues 


Epithelial tissues cover the outside of organs and structures in the body and 
line the lumens of organs in a single layer or multiple layers of cells. The 
types of epithelia are classified by the shapes of cells present and the 
number of layers of cells. Epithelia composed of a single layer of cells is 
called simple epithelia; epithelial tissue composed of multiple layers is 
called stratified epithelia. [link] summarizes the different types of 
epithelial tissues. 


Different Types of Epithelial Tissues 


Diiifesieapal ypes DEscpiplanlial Tissues Location 


Cell shape Description Location 


flat, irregular round simple: lung alveoli, 


squamous capillaries stratified: 
shape 
skin, mouth, vagina 
. h ntral 
cuboidal cube shaped, centra glands, renal tubules 
nucleus 
tall, narrow, nucleus simple: digestive tract 
columnar toward base tall, narrow, pseudostratified: 
nucleus along cell respiratory tract 
nd, simpl : 
transitional rouge, ot aple uu urinary bladder 


appear stratified 


Squamous Epithelia 


Squamous epithelial cells are generally round, flat, and have a small, 
centrally located nucleus. The cell outline is slightly irregular, and cells fit 
together to form a covering or lining. When the cells are arranged in a 
single layer (simple epithelia), they facilitate diffusion in tissues, such as 
the areas of gas exchange in the lungs and the exchange of nutrients and 
waste at blood capillaries. 


Squamous epithelia cells (a) have a slightly irregular 
shape, and a small, centrally located nucleus. These 
cells can be stratified into layers, as in (b) this human 
cervix specimen. (credit b: modification of work by 
Ed Uthman; scale-bar data from Matt Russell) 


[link]a illustrates a layer of squamous cells with their membranes joined 
together to form an epithelium. Image [link]b illustrates squamous 
epithelial cells arranged in stratified layers, where protection is needed on 
the body from outside abrasion and damage. This is called a stratified 
squamous epithelium and occurs in the skin and in tissues lining the mouth 
and vagina. 


Cuboidal Epithelia 


Cuboidal epithelial cells, shown in [link], are cube-shaped with a single, 
central nucleus. They are most commonly found in a single layer 
representing a simple epithelia in glandular tissues (e.g. pancreas, 
mammary gland, etc.). They are also found in the walls of tubules and in the 
ducts of the kidney and liver. 


Simple cuboidal 
epithelial cells line 
tubules in the 


mammalian kidney, 
where they are involved 
in filtering the blood. 


Columnar Epithelia 


Columnar epithelial cells are taller than they are wide: they resemble a 
stack of columns in an epithelial layer, and are most commonly found in a 
single-layer arrangement. The nuclei of columnar epithelial cells in the 
digestive tract appear to be lined up at the base of the cells, as illustrated in 
[link]. These cells absorb material from the lumen of the digestive tract and 
prepare it for entry into the body through the circulatory and lymphatic 
systems. 


Goblet cells 


= Columnar = = 
eau. epithelial cells ean a 


Simple columnar epithelial cells 
absorb material from the 
digestive tract. Goblet cells 
secret mucous into the digestive 
tract lumen (at top of the 
figure). 


Columnar epithelial cells lining the respiratory tract appear to be stratified. 
However, each cell is attached to the base membrane of the tissue and, 
therefore, they are simple tissues. The nuclei are arranged at different levels 
in the layer of cells, making it appear as though there is more than one 
layer, as seen in [link]. This is called pseudostratified, columnar epithelia. 
This cellular covering has cilia at the apical, or free, surface of the cells. 
The cilia enhance the movement of mucous and trapped particles out of the 
respiratory tract, helping to protect the system from invasive 
microorganisms and harmful material that has been breathed into the body. 
Goblet cells are interspersed in some tissues (such as the lining of the 
trachea). The goblet cells contain mucous that traps irritants, which in the 
case of the trachea keep these irritants from getting into the lungs. 


Goblet cells 


<a 
mm PSeudostratified — c~ 
epithelial cells 


Pseudostratified columnar 
epithelia line the 
respiratory tract. They 
exist in one layer, but the 
arrangement of nuclei at 
different levels makes it 
appear that there is more 
than one layer. Goblet 
cells interspersed between 
the columnar epithelial 
cells secrete mucous into 
the respiratory tract (at 
top of the figure). 


Connective Tissues 


Connective tissues are made up of a matrix consisting of living cells anda 
non-living substance, called the ground substance. The ground substance is 
made of an organic substance (usually a protein) and an inorganic substance 
(usually a mineral or water). The principal cell of connective tissues is the 
fibroblast. This cell makes the fibers found in nearly all of the connective 
tissues. Fibroblasts are motile, able to carry out mitosis, and can synthesize 


whichever connective tissue is needed. Macrophages, lymphocytes, and, 
occasionally, leukocytes can be found in some connective tissues. Other 
cells that can be found in different connective tissues provide functions that 
are important for those specific tissues. For example, osteocytes (found in 
bone) and adipocytes (found in fat) are specialized cells that are critical for 
the formation and function of those tissues. 


The organic portion or protein fibers found in connective tissues are either 
collagen, elastic, or reticular fibers. Collagen fibers provide strength to the 
tissue, preventing it from being torn or separated from the surrounding 
tissues. Elastic fibers are made of the protein elastin; this fiber can stretch to 
one and one half of its length and return to its original size and shape. 
Elastic fibers provide flexibility to the tissues. Reticular fibers are the third 
type of protein fiber found in connective tissues. This fiber consists of thin 
strands of collagen that form a network of fibers to support the tissue and 
other organs to which it is connected. The various types of connective 
tissues, the types of cells and fibers they are made of, and sample locations 
of the tissues is summarized in [link]. 


Connective Tissues 


Tissue Cells Fibers Location 
fibroblasts, 
macrophages, around blood 
few: collagen, 
some : vessels; 
loose/areolar elastic, 
lymphocytes, ; anchors 
reticular ; . 
some epithelia 


neutrophils 


Connective Tissues 


Tissue Cells 

dense, 

fibrous fibroblasts, 

connective macrophages, 

tissue 

chondrocytes, 

cartilage chondroblasts 
osteoblasts, 

bone osteocytes, 
osteoclasts 

adipose adipocytes 
red blood 

blood cells, white 
blood cells 


Loose/Areolar Connective Tissue 


Fibers 


mostly 
collagen 


hyaline: few 
collagen 


fibrocartilage: 


large amount 
of collagen 


some: 
collagen, 
elastic 


few 


none 


Location 


irregular: 
skin regular: 
tendons, 
ligaments 


shark 
skeleton, 
fetal bones, 
human ears, 
intervertebral 
discs 


vertebrate 
skeletons 


adipose (fat) 


blood 


Loose connective tissue, also called areolar connective tissue, has a 
sampling of all of the components of a connective tissue. As illustrated in 
[link], loose connective tissue has some fibroblasts; macrophages are 
present as well. In this figure, collagen fibers are relatively wide and stain a 
light pink, while elastic fibers are thin and stain dark blue to black. The 
space between the formed elements of the tissue is filled with the matrix. 
The material in the connective tissue gives it a loose consistency similar to 


a cotton ball that has been pulled apart. Loose connective tissue is found 
around every blood vessel and helps to keep the vessel in place. The tissue 
is also found around and between most body organs. In summary, areolar 
tissue is tough, yet flexible. 


Elastin fiber Fibroblasts Collagen fiber 


Loose connective tissue is 
composed of loosely woven 
collagen and elastic fibers. The 
fibers and other components of the 
connective tissue matrix are 
secreted by fibroblasts. 


Fibrous Connective Tissue 


Fibrous connective tissues contain large amounts of collagen fibers and few 
cells or matrix material. The fibers can be arranged irregularly or regularly 
with the strands lined up in parallel. Irregularly arranged fibrous connective 
tissues are found in areas of the body where stress occurs from all 
directions, such as the dermis of the skin. Regular fibrous connective tissue, 


shown in [link], is found in tendons (which connect muscles to bones) and 
ligaments (which connect bones to bones). 


Fibroblast nuclei Fibroblasts Collagen fibers 


Fibrous connective tissue 
from the tendon has strands 
of collagen fibers lined up 
in parallel. 


Cartilage 


Cartilage is a connective tissue with a large amount of extracellular matrix 
and variable amounts of fibers. The cells, called chondrocytes, make the 
matrix and fibers of the tissue. Chondrocytes are found in spaces within the 
tissue (lacunae). 


A cartilage with few collagen and elastic fibers is hyaline cartilage, 
illustrated in [link]. The lacunae are randomly scattered throughout the 
tissue and the matrix takes on a milky or scrubbed appearance with routine 
histological stains. Sharks have cartilaginous skeletons, as does nearly the 


entire human skeleton during a specific pre-birth developmental stage. A 
remnant of this cartilage persists in the outer portion of the human nose. 
Hyaline cartilage is also found at the ends of long bones, reducing friction 
and cushioning the articulations of these bones. 


Hyaline cartilage 
consists of a matrix 
with cells called 
chondrocytes 
embedded in it. The 
chondrocytes exist in 
cavities in the matrix 
called lacunae. 


Elastic cartilage has a large amount of elastic fibers, giving it tremendous 
flexibility. The ears of most vertebrate animals contain this cartilage as do 
portions of the larynx, or voice box. Fibrocartilage contains a large amount 
of collagen fibers, giving the tissue tremendous strength. Fibrocartilage 
comprises the intervertebral discs in vertebrate animals. Hyaline cartilage 
found in movable joints such as the knee and shoulder becomes damaged as 
a result of age or trauma. Damaged hyaline cartilage is replaced by 
fibrocartilage and results in the joints becoming “stiff.” 


Bone 


Bone, or osseous tissue, is a connective tissue that has a large amount of 
two different types of matrix material. The organic matrix is similar to the 
matrix material found in other connective tissues, including some amount of 
collagen and elastic fibers. This gives strength and flexibility to the tissue. 
The inorganic matrix consists of mineral salts—mostly calcium phosphate 
—that give the tissue hardness. In most organisms, bone is being remodeled 
by the action of cells called osteoclasts and osteoblasts (see below). 


There are three types of cells in bone: osteoblasts, osteocytes, and 
osteoclasts. Osteoblasts are active in making bone for growth and 
remodeling. Osteoblasts deposit bone material into the matrix and, after the 
matrix surrounds them, they continue to live, but in a reduced metabolic 
state as osteocytes. Osteocytes are found in lacunae of the bone. Osteoclasts 
are active in breaking down bone for bone remodeling, and they provide 
access to calcium stored in tissues. Osteoclasts are usually found on the 
surface of the tissue. 


Bone can be divided into two types: compact and spongy. Compact bone is 
found in the shaft (or diaphysis) of a long bone and the surface of the flat 
bones, while spongy bone is found in the end (or epiphysis) of a long bone. 
Compact bone is organized into subunits called osteons, as illustrated in 
[link]. A blood vessel and a nerve are found in the center of the structure 
within the Haversian canal, with radiating circles of lacunae around it 
known as lamellae. The wavy lines seen between the lacunae are 
microchannels called canaliculi; they connect the lacunae to aid diffusion 
between the cells. Spongy bone is made of tiny plates called trabeculae 
these plates serve as struts to give the spongy bone strength. Over time, 
these plates can break causing the bone to become less resilient. 


Spongy bone 


Compact “\s> 
7 N 


Lymphatic vessel 
Nerve 


Blood vessels 


Trabeculae 


Spongy bone 


x Osteocyte 
SOP IN —$— Lamellae 
peers SS (concentric circles) 
Pir Osteoclast 
Haversian 
canal 


= Canaliculi 


(canals radiating 
outward) 


Osteoblast 


LSI AKG A KH )) 
Or 
ee 


Canaliculae 


Lamellae 


(a) Compact bone is a dense matrix on the outer surface of 
bone. Spongy bone, inside the compact bone, is porous with 
web-like trabeculae. (b) Compact bone is organized into rings 
called osteons. Blood vessels, nerves, and lymphatic vessels 
are found in the central Haversian canal. Rings of lamellae 
surround the Haversian canal. Between the lamellae are 
cavities called lacunae. Canaliculi are microchannels 
connecting the lacunae together. (c) Osteoblasts surround the 


exterior of the bone. Osteoclasts bore tunnels into the bone and 
osteocytes are found in the lacunae. 


Adipose Tissue 


Adipose tissue, or fat tissue, is considered a connective tissue even though 
it does not have fibroblasts or a real matrix, and only has a few fibers. 
Adipose tissue is made up of cells called adipocytes (descendants of 
fibroblasts) that collect and store fat in the form of triglycerides. Adipose 
tissues serve as energy stores, and additionally serve as insulation to help 
maintain body temperatures, allowing animals to be endothermic. They also 
function as cushions to prevent damage to body organs. Under a 
microscope, adipose tissue cells appear empty due to the extraction of fat 
during the processing of the material for viewing, as seen in [link]. The thin 
lines in the image are the plasma membranes, and the nuclei are the small, 
black dots at the edges of the cells. 


Adipose is a connective tissue 
is made up of cells called 
adipocytes. Adipocytes have 
small nuclei localized at the 
cell edge. The interior of these 


large cells is filled with 
triglycerides, commonly known 
as "fat". 


Blood 


Blood is considered a connective tissue because it has a fluid matrix 
(plasma) and is derived from the germ layer known as mesoderm. . The 
living cell types are red blood cells (RBC), also called erythrocytes, and 
white blood cells (WBC), also called leukocytes ({link]). 


Neutrophil 


Macrophage BX & © © © 
— Monocyte 
' 
© Q Lymphocyte 
a 


® ... 
Basophil 


v9 " 
\ de @ 


© %. 


- niesd “@ 


ad 


@.% 


Platelets 


Blood is a connective tissue that has a fluid matrix, 
called plasma, and no fibers. Erythrocytes (red blood 
cells), the predominant cell type, are involved in the 
transport of oxygen and carbon dioxide. Also present 
are various leukocytes (white blood cells) involved in 

immune response. 


The cell found in greatest abundance in blood is the erythrocyte, or red 
blood cell ("erythro" = red). The principal function of an erythrocyte is to 
carry and deliver oxygen to the tissues. There are millions of erythrocytes in 
every milliliter of your blood. Mammalian erythrocytes lose their nuclei and 
mitochondria when they mature and are released from the bone marrow 
where they are generated. Fish, amphibian, and avian red blood cells 
maintain their nuclei and mitochondria throughout the cell’s life. 


Leukocytes, or white blood cells ("leuko" = white), are the other main 
cellular component of blood. There are 5,000-10,000 leukocytes in every 
milliliter of your blood. These include cells called lymphocytes, as well as 
neutrophils, monocytes, and others. Lymphocytes function primarily in the 
immune response to foreign antigens or material, which you will learn in 
more detail later in this unit. Neutrophils are phagocytic (they engulf other 
cells or objects and digest them) cells, and they participate in one of the 
early lines of defense against microbial invaders or fungal invaders. 
Another leukocyte that is found in the peripheral blood is the monocyte. 
Monocytes give rise to phagocytic macrophages that clean up dead and 
damaged cells in the body, whether they are foreign or from the host 
animal. Two additional leukocytes in the blood are eosinophils and 
basophils—both help to facilitate the inflammatory response. 


The slightly granular material among the cells in [link] are cytoplasmic 
fragments of cells formed in the bone marrow. These are called platelets or 
thrombocytes. Platelets are a key player in the formation of blood clots, 
which are important in keeping your blood in your body when you get cut 
or scraped. 


Muscle Tissues 


There are three types of muscle in animal bodies: smooth, skeletal, and 
cardiac. They differ by the presence or absence of striations or bands, the 
number and location of nuclei, whether they are voluntarily or involuntarily 
controlled, and their location within the body. [link] summarizes these 
differences. You will learn more about these cells and their functions later 
in this unit 


Types of Muscles 


Type 

of 

Muscle Striations Nuclei Control Location 

smooth no eon involuntary visceral 
many, at keletal 

skeletal yes me voluntary en 
periphery muscles 

ingle, in ; 

cardiac yes eee involuntary heart 

center 
Smooth Muscle 


Smooth muscle does not have striations in its cells. It has a single, centrally 
located nucleus, as shown in [link]. Constriction of smooth muscle occurs 
under involuntary, autonomic nervous control and in response to local 
conditions in the tissues. Smooth muscle tissue is also called non-striated as 
it lacks the banded appearance of skeletal and cardiac muscle. The walls of 
blood vessels, the tubes of the digestive system, and the tubes of the 
reproductive systems are composed of mostly smooth muscle. 


Smooth muscle cells Skeletal muscle cells Cardiac muscle cells 


————— SS 
—————— SS 
; Intercalated disc 


Smooth muscle cells do not have striations, while skeletal 
muscle cells do. Cardiac muscle cells have striations, but, 
unlike the multinucleate skeletal cells, they have only one 


nucleus. Cardiac muscle tissue also has intercalated discs, 
specialized regions running along the plasma membrane 
that join adjacent cardiac muscle cells and assist in passing 
an electrical impulse from cell to cell. 


Skeletal Muscle 


Skeletal muscle has striations across its cells caused by the arrangement of 
the contractile proteins actin and myosin. These muscle cells are relatively 
long and have multiple nuclei along the edge of the cell. Skeletal muscle is 
under voluntary, somatic nervous system control and is found in the 

muscles that move bones. [link] illustrates the histology of skeletal muscle. 


Cardiac Muscle 


Cardiac muscle, shown in [link], is found only in the heart. Like skeletal 
muscle, it has cross striations in its cells, but cardiac muscle has a single, 
centrally located nucleus. Cardiac muscle is not under voluntary control but 
can be influenced by the autonomic nervous system to speed up or slow 
down. A structure found only in cardiac muscle cells is is at the end of the 
cell where it abuts the next cardiac cell in the row. This structure is called 
an intercalated disc: it assists in passing electrical impulses efficiently from 
one cell to the next, and maintains the strong synchrony needed to make the 
heart chambers work together efficiently. 


Nervous Tissues 


Nervous tissues are made of cells specialized to receive and transmit 
electrical impulses from specific areas of the body and to send them to 
specific locations in the body. The main cell of the nervous system is the 
neuron, illustrated in [link]. The large structure with a central nucleus is the 
cell body of the neuron. Projections from the cell body are either dendrites 


specialized in receiving input or a single axon specialized in transmitting 
impulses. Some glial cells are also shown. Astrocytes regulate the chemical 
environment of the nerve cell, and oligodendrocytes insulate the axon so the 
electrical nerve impulse is transferred more efficiently. Other glial cells that 
are not shown support the nutritional and waste requirements of the neuron. 
Some of the glial cells are phagocytic and remove debris or damaged cells 
from the tissue. A nerve in your body consists of neurons and glial cells. 


Cell body (soma) 


Axon Oligodendrocyte 


Dendrites 


Astrocyte 


Axon terminals lt 


The neuron has projections called 
dendrites that receive signals and 
projections called axons that send 
signals. Also shown are two types 
of glial cells: astrocytes regulate 
the chemical environment of the 
nerve cell, and oligodendrocytes 
insulate the axon so the electrical 
nerve impulse is transferred more 
efficiently. 


Sponges and Cnidarians 


Introduction 

"Jellyfish are 97% water or something, so how much are they doing? Just 
give them another 3% and make them water. It's more useful." Karl 
Pilkington, Handslapped by a Jellyfish, 2007 

Jellyfish 


Jellyfish in the Monterey Aquarium, Monterey 
California. Image courtesy of David A. Rintoul 


Pilkington's disdain for the jellyfish (a member of the group of animals we 
call Cnidarians) is misplaced. Jellyfish, besides being spectacular and fun to 
watch, also provide food for other marine animals, including sea turtles. 
These simple animals have been around for a long time, and can also teach 
us lots of lessons about animals and animal evolution. 


The kingdom of animals is informally divided into invertebrate animals, 
those without a backbone, and vertebrate animals, those with a backbone. 
Although we are most familiar with vertebrate animals, the vast majority of 
animal species, about 95 percent, are invertebrates. Invertebrates include 


millions of species in about 32 phyla, and we will only hit the highlights in 
the subsequent sections of this text. 


The sponges and the cnidarians represent the simplest of animals. Sponges 
appear to represent an early stage of multicellularity in the animal clade. 
Although they have specialized cells for particular functions, they lack true 
tissues in which specialized cells are organized into functional groups. 
Sponges are similar to what might have been the ancestor of animals: a 
colonial, flagellated protist. The cnidarians, or the jellyfish and their kin, are 
the simplest animal group that displays true tissues, although they possess 
only two tissue layers. 


Sponges 


Animals in subkingdom Parazoa represent the simplest animals and include 
the sponges, or phylum Porifera ({link]). All sponges are aquatic and the 
majority of species are marine. Sponges live in intimate contact with water, 
which plays a role in their feeding, gas exchange, and excretion. Much of 
the body structure of the sponge is dedicated to moving water through the 
body so it can filter out food, absorb dissolved oxygen, and eliminate 
wastes. 


Sponges are members of the phylum Porifera, 
which contains the simplest animals. (credit: 
Andrew Turmer) 


The body of the simplest sponges takes the shape of a cylinder with a large 
central cavity, the spongocoel. Water enters the spongocoel from numerous 
pores in the body wall. Water flows out through a large opening called the 
osculum ([link]). However, sponges exhibit a diversity of body forms, 
which vary in the size and branching of the spongocoel, the number of 
osculi, and where the cells that filter food from the water are located. 


Sponges consist of an outer layer of flattened cells and an inner layer of 
cells called choanocytes separated by a jelly-like substance called mesohyl. 
The mesohyl contains embedded amoeboid cells that secrete tiny needles 
called spicules or protein fibers that help give the sponge its structural 
strength. The cell body of the choanocyte is embedded in mesohy]l but 
protruding into the spongocoel is a mesh-like collar surrounding a single 
flagellum. The beating of flagella from all choanocytes moves water 
through the sponge. Food particles are trapped in mucus produced by the 
sieve-like collar of the choanocytes and are ingested by phagocytosis and 


digested within those cells. Amoebocytes take up nutrients repackaged in 
food vacuoles of the choanocytes and deliver them to other cells within the 
sponge. 


Osculum 


Mesohyl 


Basic sponge body plan 


The sponge’s basic body plan is 
shown. 


Reproduction in Sponges 


Despite their lack of complexity, sponges are clearly successful organisms, 
having persisted on Earth for more than half a billion years. Lacking a true 
digestive system, sponges depend on the intracellular digestive processes of 
their choanocytes for their energy intake. The limit of this type of digestion 
is that food particles must be smaller than individual cells. Gas exchange, 
circulation, and excretion occur by diffusion between cells and the water. 


Sponges reproduce both sexually and asexually. Asexual reproduction is 
either by fragmentation (in which a piece of the sponge breaks off and 
develops into a new individual), or budding (an outgrowth from the parent 
that eventually detaches). But sponges are also capable of producing 
gametes, although both types of gametes can be produced in the same 
individual (hermaphroditism). Sponges may be sequentially 
hermaphroditic, producing eggs first and sperm later. Eggs arise from 
amoebocytes and are retained within the spongocoel, whereas sperm arise 
from choanocytes are ejected via the osculum. These sperm are carried by 
the water and fertilize the eggs of other sponges. Larval development starts 
with the sponge, and free-swimming larvae are then released via the 
osculum. This is the only time that sponges exhibit one of the hallmarks of 
the animal kingdom, motility. The larvae then attach to a substrate and 
spend their adult lives in the same spot. 


Cnidarians 


The phylum Cnidaria includes animals that show radial symmetry and are 
diploblastic (have two germ layers instead of the three). Nearly all (about 
99 percent) cnidarians are marine species, but there are freshwater jellyfish, 
even in Kansas! Cnidarians have specialized cells known as cnidocytes 
(“stinging cells”) containing organelles called nematocysts. These cells are 
concentrated around the mouth and tentacles of the animal and can 
immobilize prey with toxins. Nematocysts contain coiled threads that may 
bear barbs. The outer wall of the cell has a hairlike projection that is 
sensitive to touch. When touched, the cells fire the toxin-containing coiled 
threads that can penetrate and stun the predator or prey (see [link]). 


Touch-sensitive 
hairlike projection 


Cnidocyte X( 


Thread 


(a) Nematocyst with stored (b) Nematocyst after 
thread and barb firing 


Animals from the phylum Cnidaria have 
stinging cells called cnidocytes. Cnidocytes 
contain large organelles called (a) nematocysts 
that store a coiled thread and barb. When 
hairlike projections on the cell surface are 
touched, (b) the thread, barb, and a toxin are 
fired from the organelle. 


Cnidarians display two distinct body plans: polyp or “stalk” and medusa or 
“bell” ({link]). Examples of the polyp form are freshwater species of the 
genus Hydra; perhaps the best-known medusoid animals are the jellies 
(jellyfish). Polyps are sessile as adults, with a single opening to the 
digestive system (the mouth) facing up with tentacles surrounding it. 
Medusae are motile, with the mouth and tentacles hanging from the bell- 
shaped body. In other cnidarians, both a polyp and medusa form exist, and 
the life cycle alternates between these forms. 


Mesoglea 


(a) Medusa (b) Polyp 


Cnidarians have two distinct body plans, 
the (a) medusa and the (b) polyp. All 
cnidarians have two tissue layers, with a 
jelly-like mesoglea between them. 


Physiological Processes of Cnidarians 


All cnidarians have two tissue layers. The outer layer is called the 
epidermis, whereas the inner layer is called the gastrodermis and lines the 
digestive cavity. Between these two layers is a non-living, jelly-like 
mesoglea. There are differentiated cell types in each tissue layer, such as 
nerve cells, enzyme-secreting cells, and nutrient-absorbing cells, as well as 
intercellular connections between the cells. However, organs and organ 
systems are not present in this phylum. 


The nervous system is primitive, with nerve cells scattered across the body 
in a network. The function of the nerve cells is to carry signals from sensory 
cells and to contractile cells. Groups of cells in the nerve net form nerve 
cords that may be essential for more rapid transmission. Cnidarians perform 
extracellular digestion, with digestion completed by intracellular digestive 
processes. Food is taken into the gastrovascular cavity, enzymes are 


secreted into the cavity, and the cells lining the cavity absorb the nutrient 
products of the extracellular digestive process. The gastrovascular cavity 
has only one opening that serves as both a mouth and an anus (an 
incomplete digestive system). Like the sponges, Cnidarian cells exchange 
oxygen, carbon dioxide, and nitrogenous wastes by diffusion between cells 
in the epidermis and gastrodermis with water. 


Flatworms, Nematodes, and Arthropods 


Introduction 

"“Tn the last ten years we have come to realize humans are more like worms 
than we ever imagined.”" Bruce Alberts, American scientist and editor of 
Science magazine 


The use of a simple nematode, Caenorhabditis elegans, as a model system 
for developmental biology has indeed revealed many similarities between 
that simple creature and ourselves. The animal phyla of this and subsequent 
modules are triploblastic (i.e., have THREE primary germ layers, 
ectoderm, endoderm and mesoderm in the embryo). They have an 
embryonic mesoderm sandwiched between the ectoderm and endoderm. 
Most of these phyla are also bilaterally symmetrical, meaning that a 
longitudinal section will divide them into right and left sides that are mirror 
images of each other. Associated with bilateralism is the beginning of 
cephalization, the evolution of a concentration of nervous tissues and 
sensory organs in the head of the organism, which is where the organism 
first encounters its environment. 


The flatworms are acoelomate organisms that include free-living and 
parasitic forms. The nematodes, or roundworms, possess a pseudocoelom 
and consist of both free-living and parasitic forms. Finally, the arthropods, 
one of the most successful taxonomic groups on the planet, are coelomate 
organisms with a hard exoskeleton and jointed appendages. 


Flatworms 


Physiological Processes of Flatworms 


Most flatworms are parasitic, including important parasites of humans. 
Free-living species of flatworms are predators or scavengers, whereas 
parasitic forms feed from the tissues of their hosts. Digestion is 
extracellular, with enzymes secreted into the gut interior by cells lining the 
tract, and digested materials taken into the same cells by phagocytosis. One 
group, the cestodes, does not have a digestive system, because their 
parasitic lifestyle and the environment in which they live (suspended within 


the digestive cavity of their host) allows them to absorb nutrients directly 
across their body wall. Flatworms have an excretory system with a network 
of tubules throughout the body that open to the environment and nearby 
flame cells, whose cilia beat to direct waste fluids concentrated in the 
tubules out of the body. The system is responsible for regulation of 
dissolved salts and excretion of nitrogenous wastes. The nervous system 
consists of a pair of nerve cords running the length of the body with 
connections between them and a large ganglion or concentration of nerve 
cells at the anterior end of the worm; here, there may also be a 
concentration of photosensory and chemosensory cells ({Link]). 


Transverse 
nerve Intestine Pharynx 


Eyespot 


Cerebral ganglia 


Longitudinal nerve cords 
Peripheral nerves 


Nucleus 
Excretory canal 


Flame cell 


This planarian is a free-living flatworm that has an 
incomplete digestive system, an excretory system with a 
network of tubules throughout the body, and a nervous 
system made up of nerve cords running the length of the 
body with a concentration of nerves and photosensory 
and chemosensory cells at the anterior end. 


Since there is no circulatory or respiratory system, gas and nutrient 
exchange is dependent on diffusion and intercellular junctions. This 
necessarily limits the thickness of the body in these organisms, constraining 
them to be “flat” worms. Most flatworm species are monoecious 
(hermaphroditic, possessing both sets of sex organs), and fertilization is 
typically internal. Asexual reproduction is common in some groups in 
which an entire organism can be regenerated from just a part of itself. 


Nematodes 


The phylum Nematoda, or roundworms, includes more than 28,000 species 
with an estimated 16,000 parasitic species. The name Nematoda is derived 
from the Greek word “nemos,” which means “thread.” Nematodes are 
present in all habitats and are extremely common, although they are usually 
not visible ({link]). 


Head ganglion Cuticle Dorsalnerve Testis 


Mouth Pharynx Intestine — Ventral nerve Anus 


(b) 


(a) An scanning electron micrograph of 
the nematode Heterodera glycines and 
(b) a schematic representation of the 
anatomy of a nematode are shown. 
(credit a: modification of work by 
USDA, ARS; scale-bar data from Matt 
Russell) 


Most nematodes look similar to each other: slender tubes, tapered at each 
end ([{link]). Nematodes are pseudocoelomates and have a complete 
digestive system with a distinct mouth and anus. 


The nematode body is encased in a cuticle, a flexible but tough exoskeleton, 
or external skeleton, which offers protection and support. The cuticle 
contains a carbohydrate-protein polymer called chitin. The cuticle also lines 
the pharynx and rectum. Although the exoskeleton provides protection, it 
restricts growth, and therefore must be continually shed and replaced as the 
animal increases in size. 


A nematode’s mouth opens at the anterior end with three or six lips and, in 
some species, teeth in the form of cuticular extensions. There may also be a 
sharp stylet that can protrude from the mouth to stab prey or pierce plant or 
animal cells. The mouth leads to a muscular pharynx and intestine, leading 
to the rectum and anal opening at the posterior end. 


Physiological Processes of Nematodes 


In nematodes, the excretory system is not specialized. Nitrogenous wastes 
are removed by diffusion. In marine nematodes, regulation of water and salt 
is achieved by specialized glands that remove unwanted ions while 
maintaining internal body fluid concentrations. 


Most nematodes have four nerve cords that run along the length of the body 
on the top, bottom, and sides. The nerve cords fuse in a ring around the 
pharynx, to form a head ganglion or “brain” of the worm, as well as at the 
posterior end to form the tail ganglion. Beneath the epidermis lies a layer of 
longitudinal muscles that permits only side-to-side, wave-like undulation of 
the body. 


Nematodes employ a diversity of sexual reproductive strategies depending 
on the species; they may be monoecious, dioecious (Separate sexes), or may 
reproduce asexually by parthenogenesis. Caenorhabditis elegans is nearly 
unique among animals in having both self-fertilizing hermaphrodites and a 
male sex that can mate with the hermaphrodite. 


Arthropoda 


The name of this phylum, “Arthropoda” means “jointed legs,” which aptly 
describes each of the enormous number of species belonging to this 
phylum. An estimated 85 percent of known species belong to this phylum, 
with many more still undiscovered or undescribed. Insects form the largest 
single group within the phylum. The principal characteristics of all the 
animals in this phylum are functional segmentation of the body and the 
presence of jointed appendages ([link]). Arthropods also have an 
exoskeleton made principally of chitin. Arthropods are true coelomate 
animals and exhibit protostomic development. 


Trilobites, like the one in this fossil, are 
an extinct group of arthropods. (credit: 
Kevin Walsh) 


Physiological Processes of Arthropods 


A unique feature of arthropods is the presence of a segmented body with 
fusion of certain sets of segments to give rise to functional segments. Fused 
segments may form a head, thorax, and abdomen, or a cephalothorax and 
abdomen, or a head and trunk. The coelom takes the form of a hemocoel (or 
blood cavity). The open circulatory system, in which blood bathes the 


internal organs rather than circulating in vessels, is powered by a two- 
chambered heart. Respiratory systems vary, depending on the group of 
arthropod: Insects and myriapods use a series of tubes (tracheae) that 
branch throughout the body, open to the outside through openings called 
spiracles, and perform gas exchange directly between the cells and air in the 
tracheae. Aquatic crustaceans use gills, arachnids employ “book lungs,” and 
aquatic chelicerates use “book gills.” The book lungs of arachnids are 
internal stacks of alternating air pockets and hemocoel tissue shaped like 
the pages of a book. The book gills of crustaceans are external structures 
similar to book lungs with stacks of leaf-like structures that exchange gases 
with the surrounding water ([link]). 


Book gills 


Cephalothorax 


Book lung 


(a) (b) 


The book lungs of (a) arachnids are made up of 
alternating air pockets and hemocoel tissue shaped like a 
stack of books. The book gills of (b) crustaceans are 
similar to book lungs but are external so that gas 
exchange can occur with the surrounding water. (credit a: 
modification of work by Ryan Wilson based on original 
work by John Henry Comstock; credit b: modification of 
work by Angel Schatz) 


Arthropod Diversity 


Phylum Arthropoda includes animals that have been successful in 
colonizing terrestrial, aquatic, and aerial habitats. The phylum is further 
classified into five subphyla: Trilobitomorpha (trilobites), Hexapoda 
(insects and relatives), Myriapoda (millipedes, centipedes, and relatives), 
Crustacea (crabs, lobsters, crayfish, isopods, barnacles, and some 
zooplankton), and Chelicerata (horseshoe crabs, arachnids, scorpions, and 
daddy longlegs). Trilobites are an extinct group of arthropods found from 
the Cambrian period (540—490 million years ago) until they became extinct 
in the Permian (300-251 million years ago) that are probably most closely 
related to the Chelicerata. The 17,000 described species have been 
identified from fossils ([link]). 


Abdomen Thorax 


Head 


Dorsal blood 
vessel Cerebral 
AN) ganglion 


Anus 
Intestine 


Spiracles 


The basic anatomy of a representative 
arthropod, in this case an insect, or 
hexapod. Note that insects have a 
developed digestive system (yellow), a 
respiratory system (blue), a circulatory 
system (red), and a nervous system 


(purple). 


Mollusks and Annelids 


Introduction 

"Clams are very conservative. They voted against having heads in the 
Ordovician Period and have stuck to it ever since." Will Cuppy, American 
humorist, in How to Attract the Wombat, 1949 


The mollusks are a diverse group (85,000 described species) of mostly 
marine species. They have a variety of forms, ranging from large predatory 
squid and octopus, some of which show a high degree of intelligence, to 
small grazing forms with elaborately sculpted and colored shells. The 
annelids traditionally include the oligochaetes, which include the 
earthworms and leeches, the polychaetes, which are a marine group, and 
two other smaller classes. 


Phylum Mollusca 


An Edible Mollusk 


Some mollusks are edible, like these Black Abalone (Haliotis 
cracherodii), cruising in a tide pool of the coast of California. This 
gastropod mollusk shows several of the features of many members of 
this phylum, including a sturdy shell and a muscular foot. However, 
due to overharvesting of this species, its populations are declining 
and it can no longer be legally taken. "Abalone OCA" by Little 
Mountain 5 - Own work. Licensed under Creative Commons 
Attribution-Share Alike 3.0 via Wikimedia Commons. 


Mollusca is the predominant phylum in marine environments; it is 
estimated that 23 percent of all known marine species belong to this 
phylum. It is the second most diverse phylum of animals with over 75,000 
described species. The name “mollusca” signifies a soft body, as the earliest 
descriptions of mollusks came from observations of unshelled, soft-bodied 


cuttlefish (squid relatives). Although mollusk body forms vary, they share 
key characteristics, such as a ventral, muscular foot that is typically used for 
locomotion; the visceral mass, which contains most of the internal organs of 
the animal; and a dorsal mantle, which is a flap of tissue over the visceral 
mass that creates a space called the mantle cavity. The mantle may or may 
not secrete a shell of calcium carbonate. In addition, many mollusks have a 
scraping structure at the mouth, called a radula ([Link]). 


The muscular foot varies in shape and function, depending on the type of 
mollusk. It is a retractable as well as extendable organ, used for locomotion 
and anchorage. Mollusks are eucoelomates, but the coelomic cavity is 
restricted to a cavity around the heart in adult animals. The mantle cavity, 
formed inside the mantle, develops independently of the coelomic cavity. It 
is a multi-purpose space, housing the gills, the anus, organs for sensing food 
particles in the water, and an outlet for gametes. Most mollusks have an 
open circulatory system with a heart that circulates the hemolymph in open 
Spaces around the organs. The octopuses and squid are an exception to this 
and have a closed circulatory system with two hearts that move blood 
through the gills and a third, systemic heart that pumps blood through the 
rest of the body. 


Mantle Coelom Intestine Gonad Shell 


Anus 


Digestive 
gland 


Stomach 


Foot 
Mouth 


Nerve Visceral 
Radula cords Crop mass Heart 


There are many species and variations of 
mollusks; the gastropod mollusk anatomy 
is shown here, which shares many 


characteristics common with other 
groups. 


Annelida 


Phylum Annelida are segmented worms found in marine, terrestrial, and 
freshwater habitats, but the presence of water or humidity is a critical factor 
for their survival in terrestrial habitats. The name of the phylum is derived 
from the Latin word annellus, which means a small ring. Approximately 
16,500 species have been described. The phylum includes earthworms, 
polychaete worms, and leeches. Like mollusks, annelids exhibit protostomic 
development. 


Annelids are bilaterally symmetrical and have a worm-like appearance. 
Their particular segmented body plan results in repetition of internal and 
external features in each body segment. This type of body plan is called 
metamerism. The evolutionary benefit of such a body plan is thought to be 
the capacity it allows for the evolution of independent modifications in 
different segments that perform different functions. The overall body can 
then be divided into head, body, and tail. 


Physiological Processes of Annelida 


The skin of annelids is protected by a cuticle that is thinner than the cuticle 
of nematodes and arthropods, and it does not need to be molted for growth. 
Chitinous hairlike extensions, anchored in the skin and projecting from the 
cuticle, called chaetae, are present in every segment in most groups. The 
chaetae are a defining character of annelids. Beneath the cuticle there are 
two layers of muscle, one running around its circumference (circular) and 
one running the length of the worm (longitudinal). Annelids have a true 
coelom in which organs are distributed and bathed in coelomic fluid. 
Annelids possess a well-developed complete digestive system with 
specialized organs: mouth, muscular pharynx, esophagus, and crop. A 
cross-sectional view of a body segment of an earthworm is shown in [link]; 
each segment is limited by a membrane that divides the body cavity into 
compartments. 


Annelids have a closed circulatory system with muscular pumping “hearts” 
in the anterior segments, dorsal and ventral blood vessels that run the length 
of the body with connections in each segment, and capillaries that service 
individual tissues. Gas exchange occurs across the moist body surface. 
Excretion is carried out by pairs of primitive “kidneys” called 
metanephridia that consist of a convoluted tubule and an open, ciliated 
funnel present in every segment. Annelids have a well-developed nervous 
system with two ventral nerve cords and a nerve ring of fused ganglia 
present around the pharynx. 


Dorsal blood vessel 


Chaetae 


Nephridium 


Intestine Ventral blood vessel 


Ventral nerve cord 


In this schematic showing the basic 
anatomy of annelids, the digestive system 
is indicated in green, the nervous system 
is indicated in yellow, and the circulatory 

system is indicated in red. 


Annelids may be either monoecious (hermaphroditic, capable of producing 
both male and female gametes), such as earthworms and leeches) or 
dioecious (indivduals are either male or female), as is the case for 
polychaetes. 


Echinoderms and Chordates 


Introduction 

"Here’s a little lesson in deuterostome taxonomy for everyone out there. 
These are animals in which the first embryonic opening become the anus, 
and the second opening becomes the mouth (the name literally means 
mouth second). This is in contrast the majority of animals, which form their 
mouth first." RPM, author of the Evolgen blog, 2008 


The phyla Echinodermata and Chordata (which includes the vertebrates) 
and two smaller phyla are the members of the Deuterstomes. Deuterostomes 
share similar patterns of early development, as noted above, which 
distinguish them from most of the other animals. 


Echinoderms 


Echinodermata are named for their spiny skin (from the Greek “echinos” 
meaning “spiny” and “dermos” meaning “skin”). The phylum includes 
about 7,000!22D9te] described living species, such as sea stars, sea 
cucumbers, sea urchins, sand dollars, and brittle stars. Echinodermata are 
exclusively marine. 

“Number of Living Species in Australia and the World,” A.D. Chapman, 
Australia Biodiversity Information Services, last modified August 26, 2010, 
http://www.environment.gov.au/biodiversity/abrs/publications/other/species 
-numbers/2009/03-exec-summary.html. 


Although the early larval stages of all echinoderms have bilateral symmetry, 
adult echinoderms exhibit pentaradial symmetry and have an endoskeleton 
made of ossicles ([{link]). The endoskeleton is developed by epidermal cells, 
which may also possess pigment cells, giving vivid colors to these animals, 
as well as cells laden with toxins. These animals have a true coelom, a 
portion of which is modified into a unique circulatory system called a water 
vascular system. An interesting feature of these animals is their power to 
regenerate, even when over 75 percent of their body mass is lost. 


Physiological Processes of Echinoderms 


Echinoderms have a unique system for gas exchange, nutrient circulation, 
and locomotion called the water vascular system. The system consists of a 
central ring canal and radial canals extending along each arm. Water 
circulates through these structures allowing for gas, nutrient, and waste 
exchange. A structure on top of the body, called the madreporite, regulates 
the amount of water in the water vascular system. “Tube feet,” which 
protrude through openings in the endoskeleton, may be expanded or 
contracted using the hydrostatic pressure in the system. The system allows 
for slow movement, but a great deal of power, as witnessed when the tube 
feet latch on to opposite halves of a bivalve mollusk, like a clam, and 
slowly, but surely pull the shells apart, exposing the flesh within. 


Madreporite 


Central ring canal 


Digestive glands 


This diagram shows the anatomy of a sea Star. 


The echinoderm nervous system has a nerve ring at the center and five 
radial nerves extending outward along the arms. There is no centralized 
nervous control. Echinoderms have separate sexes and release their gametes 
into the water where fertilization takes place. Echinoderms may also 
reproduce asexually through regeneration from body parts. 


Echinoderm Diversity 


This phylum is divided into five classes: Asteroidea (sea stars), Ophiuroidea 
(brittle stars), Echinoidea (sea urchins and sand dollars), Crinoidea (sea 
lilies or feather stars), and Holothuroidea (sea cucumbers) ([link]). 


(d) 


Different members of Echinodermata include the (a) sea 
star in class Asteroidea, (b) the brittle star in class 
Ophiuroidea, (c) the sea urchins of class Echinoidea, (d) 
the sea lilies belonging to class Crinoidea, and (d) sea 
cucumbers representing class Holothuroidea. (credit a: 
modification of work by Adrian Pingstone; credit b: 
modification of work by Joshua Ganderson; credit c: 
modification of work by Samuel Chow; credit d: 
modification of work by Sarah Depper; credit e: 
modification of work by Ed Bierman) 


Chordates 


The majority of species in the phylum Chordata are found in the subphylum 
Vertebrata, which include many species with which we are familiar. The 
vertebrates contain more than 60,000 described species, divided into major 
groupings of the lampreys, fishes, amphibians, reptiles, birds, and 
mammals. 


Animals in the phylum Chordata share four key features that appear at 
some stage of their development: a notochord, a dorsal hollow nerve cord, 
pharyngeal slits, and a post-anal tail ({link]). In certain groups, some of 
these traits are present only during embryonic development. 


The chordates are named for the notochord, which is a flexible, rod-shaped 
structure that is found in the embryonic stage of all chordates and in the 
adult stage of some chordate species. It is located between the digestive 
tube and the nerve cord, and provides skeletal support through the length of 
the body. In some chordates, the notochord acts as the primary axial support 
of the body throughout the animal’s lifetime. In vertebrates, the notochord 
is present during embryonic development, at which time it induces the 
development of the neural tube and serves as a support for the developing 
embryonic body. The notochord, however, is not found in the postnatal 
stage of vertebrates; at this point, it has been replaced by the vertebral 
column (the spine). 


The dorsal hollow nerve cord is derived from ectoderm that sinks below 
the surface of the skin and rolls into a hollow tube during development. In 
chordates, it is located dorsally to the notochord. In contrast, other animal 
phyla possess solid nerve cords that are located either ventrally or laterally. 
The nerve cord found in most chordate embryos develops into the brain and 
spinal cord, which compose the central nervous system. 


Pharyngeal slits are openings in the pharynx, the region just posterior to 
the mouth, that extend to the outside environment. In organisms that live in 
aquatic environments, pharyngeal slits allow for the exit of water that enters 
the mouth during feeding. Some invertebrate chordates use the pharyngeal 
slits to filter food from the water that enters the mouth. In fishes, the 
pharyngeal slits are modified into gill supports, and in jawed fishes, jaw 


supports. In tetrapods, the slits are further modified into components of the 
ear and tonsils, since there is no longer any need for gill supports in these 
air-breathing animals. Tetrapod means “four-footed,” and this group 
includes amphibians, reptiles, birds, and mammals. (Birds are considered 
tetrapods because they evolved from tetrapod ancestors.) 


The post-anal tail is a posterior elongation of the body extending beyond 
the anus. The tail contains skeletal elements and muscles, which provide a 
source of locomotion in aquatic species, such as fishes. In some terrestrial 
vertebrates, the tail may also function in balance, locomotion, courting, and 
signaling when danger is near. In many species, the tail is absent or 
reduced; for example, in apes, including humans, it is present in the 
embryo, but reduced in size and nonfunctional in adults. 


Dorsal hollow 
nerve cord 


Notochord Post-anal tail 


Pharyngeal slits 


In chordates, four common features 
appear at some point in development: a 
notochord, a dorsal hollow nerve cord, 

pharyngeal slits, and a post-anal tail. The 
anatomy of a cephalochordate shown here 
illustrates all of these features. 


Invertebrate Chordates 


In addition to the vertebrates, the phylum Chordata contains two clades of 
invertebrates: Urochordata (tunicates) and Cephalochordata (lancelets). 
Members of these groups possess the four distinctive features of chordates 
at some point during their development. 


The tunicates ([link]) are also called sea squirts. The name tunicate derives 
from the cellulose-like carbohydrate material, called the tunic, which covers 
the outer body. Although tunicates are classified as chordates, the adult 
forms are much modified in body plan and do not have a notochord, a 
dorsal hollow nerve cord, or a post-anal tail, although they do have 
pharyngeal slits. The larval form possesses all four structures. Most 
tunicates are hermaphrodites. Tunicate larvae hatch from eggs inside the 
adult tunicate’s body. After hatching, a tunicate larva swims for a few days 
until it finds a suitable surface on which it can attach, usually in a dark or 
shaded location. It then attaches by the head to the substrate and undergoes 
metamorphosis into the adult form, at which point the notochord, nerve 
cord, and tail disappear. 


Mouth Anus Dorsal hollow 


nerve cord Pharyngeal 


slits 
Tunic 


Anus 
Heart 


Pharyngeal Stomach Notocord 
slits 


Stomach Gonad 


(a) (b) (c) 


(a) This photograph shows a colony of the tunicate Botrylloides 
violaceus. In the (b) larval stage, the tunicate can swim freely until it 
attaches to a substrate to become (c) an adult. (credit a: modification 

of work by Dr. Dwayne Meadows, NOAA/NMFS/OPR) 


Lancelets possess a notochord, dorsal hollow nerve cord, pharyngeal slits, 
and a post-anal tail in the adult stage ([link]). The notochord extends into 


the head, which gives the subphylum its name (Cephalochordata). Extinct 
fossils of this subphylum date to the middle of the Cambrian period (540— 
488 mya).The living forms, the lancelets, are named for their blade-like 
shape. Lancelets are only a few centimeters long and are usually found 
buried in sand at the bottom of warm temperate and tropical seas. Like 
tunicates, they are suspension feeders. 


Adult lancelets retain the four key 
features of chordates: a notochord, a 
dorsal hollow nerve cord, pharyngeal 

slits, and a post-anal tail. 


Vertebrates 


Introduction 

"The development of the Vertebrate proceeds from an axis upward, in two 
layers, which coalesce at the edges, and also downward, in two layers, 
which likewise coalesce at the edges. Thus two main tubes are formed, one 
above the other. During the formation of these, the embryo separates into 
strata, so that the two main tubes are composed of subordinate tubes which 
enclose each other as fundamental organs, and are capable of developing 
into all the organs." Karl Ernst von Baer, German embryologist, 1828 


Vertebrates are the largest and probably the most recognizable organisms of 
the animal kingdom ([link]). More than 62,000 vertebrate species have been 
identified. The vertebrate species now living represent only a small portion 
of the vertebrates that have existed. The best-known extinct vertebrates are 
the dinosaurs, a unique group of reptiles, reaching sizes not seen before or 
since in terrestrial animals. 


(a) (b) (c) 


Examples of critically endangered vertebrate species include 
(a) the Siberian tiger (Panthera tigris altaica), (b) the 
Panamanian golden frog (Atelopus zeteki), and (c) the 

Philippine eagle (Pithecophaga jefferyi). (credit a: modification 
of work by Dave Pape; credit b: modification of work by Brian 
Gratwicke; credit c: modification of work by 
"cuatrok77"/Flickr) 


Fishes 


Modern fishes include an estimated 31,000 species. Fishes were the earliest 
vertebrates, and jawless fishes were the earliest of these. Jawless fishes— 
the present day hagfishes and lampreys—have a distinct cranium and 
complex sense organs including eyes, distinguishing them from the 
invertebrate chordates. The jawed fishes evolved later and are 
extraordinarily diverse today. These include the cartilaginous fishes (e.g. 
rays and sharks), with a skeleton made of cartilage, and the bony fishes, 
which have a bony skeleton. All fishes are active feeders, rather than 
sessile, suspension feeders. 


Jawless fishes 


Jawless fishes 


ey 


ae = : 


(a) Jawless fishes include 67 species of hagfishes. These 
Pacific hagfishes are scavengers that live on the ocean floor. 
(b) Lampreys are another type of jawless fish. These parasitic 
sea lampreys attach to their lake trout host by suction and use 
their rough tongues to rasp away flesh in order to feed on the 
trout’s blood. (credit a: modification of work by Linda Snook, 
NOAA/CBNMS; credit b: modification of work by USGS) 


Jawed fishes 


Cartilaginous fishes 


(a) 


The jawed fishes include the clade Chondrichthyes, fishes with 
skeletons made of cartilage, and these include the sharks and 
rays(a) This hammerhead shark is an example of a predatory 

cartilaginous fish. (b) This stingray blends into the sandy 
bottom of the ocean floor when it is feeding or awaiting prey. 

(credit a: modification of work by Masashi Sugawara; credit b: 

modification of work by "Sailn1"/Flickr) 


Sharks reproduce sexually and eggs are fertilized internally. Most species 
are ovoviviparous, that is, the fertilized egg is retained in the oviduct of the 
mother’s body, and the embryo is nourished by the egg yolk. The eggs 
hatch in the uterus and young are born alive and fully functional. Some 
species of sharks are oviparous: They lay eggs that hatch outside of the 
mother’s body. Embryos are protected by a shark egg case or “mermaid’s 
purse” that has the consistency of leather. The shark egg case has tentacles 
that snag in seaweed and give the newborn shark cover. A few species of 
sharks are viviparous, that is, the young develop within the mother’s body, 
and she gives live birth. 


Rays and skates include more than 500 species and are closely related to 
sharks. They can be distinguished from sharks by their flattened bodies, 
pectoral fins that are enlarged and fused to the head, and gill slits on their 
ventral surface ({link]b). Like sharks, rays and skates have a cartilaginous 


skeleton. Most species are marine and live on the sea floor, with nearly a 
worldwide distribution. 


Bony Fishes 


Members of the clade Osteichthyes, or bony fishes, are characterized by a 
bony skeleton. The vast majority of present-day fishes belong to this group, 
which consists of approximately 30,000 species, making it the largest class 
of vertebrates in existence today. 


(a) (b) 


The (a) sockeye salmon and (b) coelacanth are both bony 
fishes of the Osteichthyes clade. The coelacanth, 
sometimes called a lobe-finned fish, was thought to have 
gone extinct in the Late Cretaceous period 100 million 
years ago until one was discovered in 1938 between 
Africa and Madagascar. (credit a: modification of work 
by Timothy Knepp, USFWS; credit b: modification of 
work by Robbie Cada) 


Amphibians 


Amphibians are vertebrate tetrapods. Amphibia includes the familiar frogs, 
toads, and salamanders, as well as the caecilians, limbless amphibians that 
superficially resemble worms and snakes. The term amphibian means “dual 
life,” which is a reference to the metamorphosis that many frogs undergo 
from a tadpole to an adult and the mixture of aquatic and terrestrial 


environments in their life cycle. Amphibians evolved in the Devonian 
period and were the earliest terrestrial tetrapods. 


Amphibian Diversity 


Amphibia comprise an estimated 6,500 extant species that inhabit tropical 
and temperate regions around the world. Amphibians can be divided into 
three clades: Urodela (“tailed-ones”’), the salamanders and newts; Anura 
(“tail-less ones”), the frogs and toads; and Apoda (“legless ones”), the 
caecilians. 

Frogs and Salamanders 


(a) (b) 


There are about 500 species of salamanders and 5,000 
species of frogs worldwide. (a) Salamanders are 
terrestrial animals, but most are commonly found only 
near water. (b) The Australian green tree frog is a 
nocturnal predator that lives in the canopies of trees near 
a water source. (credit a: modification of work by 
Valentina Storti; credit b: modification of work by Evan 
Pickett) 


Caecilians comprise an estimated 185 species. They lack external limbs and 
resemble giant earthworms. They inhabit soil and are found primarily in the 
tropics of South America, Africa, and southern Asia where they are adapted 
for a soil-burrowing lifestyle and are nearly blind. Unlike most of the other 
amphibians that breed in or near water, reproduction in a drier soil habitat 


means that caecilians must utilize internal fertilization, and most species 
give birth to live young ((link]). 


Caecilians lack external limbs and are 
well adapted for a soil-burrowing 
lifestyle. (credit: modification of work by 
"cliff1066"/Flickr) 


Reptiles and Birds 


The amniotes—reptiles, birds, and mammals—are distinguished from 
amphibians by their terrestrially adapted (shelled) egg and an embryo 
protected by amniotic membranes. The evolution of amniotic membranes 
meant that the embryos of amniotes could develop within an aquatic 
environment inside the egg. This led to less dependence on a water 
environment for development and allowed the amniotes to invade drier 
areas. This was a significant evolutionary change that distinguished them 
from amphibians, which were restricted to moist environments due to their 
shell-less eggs. Although the shells of various amniotic species vary 
significantly, they all allow retention of water. The membranes of the 
amniotic egg also allowed gas exchange and sequestering of wastes within 
the enclosure of an eggshell. The shells of bird eggs are composed of 
calcium carbonate and are hard and brittle, but possess pores for gas and 
water exchange. The shells of reptile eggs are more leathery and pliable. 


Most mammals do not lay eggs; however, even with internal gestation, 
amniotic membranes are still present. 


In the past, the most common division of amniotes has been into classes 
Mammalia, Reptilia, and Aves. Birds are descended, however, from 
dinosaurs, so this classical scheme results in groups that are not true clades. 
We will discuss birds as a group distinct from reptiles with the 
understanding that this does not reflect evolutionary history. 


Reptiles 


Reptiles are tetrapods. Limbless reptiles—snakes—may have vestigial 
limbs and, like caecilians, are classified as tetrapods because they are 
descended from four-limbed ancestors. Reptiles lay shelled eggs on land. 
Even aquatic reptiles, like sea turtles, return to the land to lay eggs. They 
usually reproduce sexually with internal fertilization. Some species display 
Ovoviviparity, with the eggs remaining in the mother’s body until they are 
ready to hatch. Other species are viviparous, with the offspring born alive. 


One of the key adaptations that permitted reptiles to live on land was the 
development of their scaly skin, containing the protein keratin and waxy 
lipids, which prevented water loss from the skin. This occlusive skin means 
that reptiles cannot use their skin for respiration, like amphibians, and thus 
all must breathe with lungs. In addition, reptiles conserve valuable body 
water by excreting nitrogen in the form of uric acid paste. These 
characteristics, along with the shelled, amniotic egg, were the major reasons 
why reptiles became so successful in colonizing a variety of terrestrial 
habitats far from water. 


Reptiles are ectotherms, that is, animals whose main source of body heat 
comes from the environment. Behavioral maneuvers, like basking to heat 
themselves, or seeking shade or burrows to cool off, help them regulate 
their body temperature, 


Class Reptilia includes diverse species classified into four living clades. 
These are the Crocodilia, Sphenodontia, Squamata, and Testudines. 


The Crocodilia (“small lizard”) arose approximately 84 million years ago, 
and living species include alligators, crocodiles, and caimans. Crocodilians 
({link]a) live throughout the tropics of Africa, South America, the 
southeastern United States, Asia, and Australia. They are found in 
freshwater habitats, such as rivers and lakes, and spend most of their time in 
water. Some species are able to move on land due to their semi-erect 
posture. 


4f Abs yd 


(a) Crocodilians, such as this Siamese crocodile, provide 
parental care for their offspring. (b) This Tuatara 
(Sphenodon punctatus is one of only two species in the 
Sphenodontia, and is found only in New Zealand. (c) 
The garter snake belongs to the genus Thamnophis, the 
most widely distributed reptile genus in North America. 
(d) The African spurred tortoise lives at the southern 
edge of the Sahara Desert. It is the third largest tortoise 


in the world. (credit a: modification of work by Keshav 
Mukund Kandhadai; credit b: courtesy of David A. 
Rintoul; credit c: modification of work by Steve 
Jurvetson; credit d: modification of work by Jim Bowen) 


The Sphenodontia (“wedge tooth”) arose in the Mesozoic Era and includes 
only one living genus, the Tuatara, with two species that are found in New 
Zealand ([{link]b). There are many fossil species extending back to the 
Triassic period (250-200 million years ago). Although the tuataras resemble 
lizards, they are anatomically distinct and share characteristics that are 
found in birds and turtles. 


Squamata (“scaly”) arose in the late Permian; living species include lizards 
and snakes, which are the largest extant clade of reptiles. Lizards differ 
from snakes by having four limbs, eyelids, and external ears, which are 
lacking in snakes. Lizard species range in size from chameleons and geckos 
that are a few centimeters in length to the Komodo dragon, which is about 3 
meters in length. 


Snakes are thought to have descended from either burrowing lizards or 
aquatic lizards over 100 million years ago ([{link]c). Snakes comprise about 
3,000 species and are found on every continent except Antarctica. They 
range in size from 10 centimeter-long thread snakes to 7.5 meter-long 
pythons and anacondas. All snakes are carnivorous and eat small animals, 
birds, eggs, fish, and insects. 


Turtles are members of the clade Testudines (“having a shell”) ({link]d). 
Turtles are characterized by a bony or cartilaginous shell, made up of the 
carapace on the back and the plastron on the ventral surface, which 
develops from the ribs. Turtles arose approximately 200 million years ago, 
predating crocodiles, lizards, and snakes. Turtles lay eggs on land, although 
many species live in or near water. Turtles range in size from the speckled 
padloper tortoise at 8 centimeters (3.1 inches) to the leatherback sea turtle at 
200 centimeters (over 6 feet). The term “turtle” is sometimes used to 
describe only those species of Testudines that live in the sea, with the terms 


“tortoise” and “terrapin” used to refer to species that live on land and in 
fresh water, respectively. 


Birds 


Fossil and genomic data now suggest that birds belong within the reptile 
clade, but they display a number of unique adaptations that set them apart. 
Unlike the reptiles, birds are endothermic, meaning they generate their own 
body heat through metabolic processes. The most distinctive characteristic 
of birds is their feathers, which are modified reptilian scales. Birds have 
several different types of feathers that are specialized for specific functions, 
like contour feathers that streamline the bird’s exterior and loosely 
structured down feathers that insulate ([link]a). Current thinking is that 
some dinosaurs (the ancestors of modern birds) were also endothermic. 


Feathers not only permitted the earliest birds to glide, and ultimately engage 
in flapping flight, but they insulated the bird’s body, assisting the 
maintenance of endothermy, even in cooler temperatures. Powering a flying 
animal requires economizing on the amount of weight carried. As body 
weight increases, the muscle output and energetic cost required for flying 
increase. Birds have made several modifications to reduce body weight, 
including hollow or pneumatic bones ([link]b) with air spaces that may be 
connected to air sacs and cross-linked struts within their bones to provide 
structural reinforcement. Parts of the vertebral skeleton and braincase are 
fused to increase its strength while lightening its weight. Most species of 
bird only possess one ovary rather than two, and no living birds have teeth 
in their jaw, further reducing body mass. 


Primary 
feathers 


Secondary 
feathers 


att xe) 
Nal New 


(a) 


(a) Primary feathers are located at the wing tip and 
provide thrust; secondary feathers are located close to 
the body and provide lift. (b) Many birds have hollow 

pneumatic bones, which make flight easier. 


Birds possess a system of air sacs branching from their primary airway that 
divert the path of air so that it passes unidirectionally through the lung, 
during both inspiration and expiration. Unlike mammalian lungs in which 
air flows in two directions as it is breathed in and out, air flows 
continuously through the bird’s lung to provide a more efficient system of 
gas exchange. 


Mammals 


Mammals are vertebrates that have hair and mammary glands used to 
provide nutrition for their young. Certain features of the jaw, skeleton, skin, 
and internal anatomy are also unique to mammals. The presence of hair is 
one of the key characteristics of a mammal. Although it is not very 
extensive in some groups, such as whales, hair has many important 
functions for mammals. Mammals are endothermic, and hair provides 


insulation by trapping a layer of air close to the body to retain metabolic 
heat. Hair also serves as a sensory mechanism through specialized hairs 
called vibrissae, better known as whiskers. These attach to nerves that 
transmit touch information, which is particularly useful to nocturnal or 
burrowing mammals. Hair can also provide protective coloration. 


The skeletal system of mammals possesses unique features that differentiate 
them from other vertebrates. Most mammals have heterodont teeth, 
meaning they have different types and shapes of teeth that allow them to 
feed on different kinds of foods. These different types of teeth include the 
incisors, the canines, premolars, and molars. The first two types are for 
cutting and tearing, whereas the latter two types are for crushing and 
grinding. Different groups have different proportions of each type, 
depending on their diet. Most mammals are also diphyodonts, meaning they 
have two sets of teeth in their lifetime: deciduous or “baby” teeth, and 
permanent teeth. In other vertebrates, the teeth can be replaced throughout 
life. 


Modern mammals are divided into three broad groups: monotremes, 
marsupials, and eutherians (mammals with a placenta). The eutherians and 
the marsupials collectively are called therian mammals, whereas 
monotremes are called metatherians. 


There are three living species of monotremes: the platypus and two species 
of echidnas, or spiny anteaters (({link]). The platypus and one species of 
echidna are found in Australia, whereas the other species of echidna is 
found in New Guinea. Monotremes are unique among mammals, as they lay 
leathery eggs, similar to those of reptiles, rather than giving birth to live 
young. However, the eggs are retained within the mother’s reproductive 
tract until they are almost ready to hatch. Once the young hatch, the female 
begins to secrete milk from pores in a ridge of mammary tissue along the 
ventral side of her body. Like other mammals, monotremes are endothermic 
but regulate body temperatures somewhat lower (90 °F, 32 °C) than 
placental mammals do (98 °F, 37 °C). 


The platypus (left), a monotreme, possesses a leathery 
beak and lays eggs rather than giving birth to live young. 
An echidna, another monotreme, is shown in the right 
photo. (credit “echidna”: modification of work by Barry 
Thomas) 


Marsupials are found primarily in Australia and nearby islands, although 
about 100 species of opossums and a few species of two other families are 
found in the Americas. Australian marsupials number over 230 species and 
include the kangaroo, koala, bandicoot, and Tasmanian devil ({link]). Most 
species of marsupials possess a pouch in which the young reside after birth, 
receiving milk and continuing to develop. Before birth, marsupials have a 
less complex placental connection, and the young are born much less 
developed than in placental mammals. 


The Tasmanian devil is one of several 
marsupials native to Australia. (credit: 
Wayne McLean) 


Eutherian Diversity 


(d) 


Four eutherian mammals: A. A chiropteran, the Mexican Long- 
tongued Bat (Choeronycteris mexicana) feeding on sugar water at a 
hummingbird feeder. These bats pollinate many varieties of cactuses 
and agaves, including the blue agave that is used to make tequila. B. 
Pink River Dolphin (Inia geoffrensis), a freshwater cetacean found in 

the Amazon River and its tributaries. C. A xenarthran, the Giant 
Anteater or Tamandua (Tamandua tetradactyla), hunting for termites 
in the Pantanal of Brazil. D. A member of the order Carnivora, the 
Domestic Cat (Felis catus). Photo credits - David A. Rintoul 


Eutherians are the most widespread of the mammals, occurring throughout 
the world. There are several groups of eutherians, including Insectivora, the 
insect eaters; Xenarthra, the toothless anteaters; Rodentia, the rodents; 


Chiroptera, the bats; Cetacea, the aquatic mammals including whales; 
Carnivora, carnivorous mammals including dogs, cats, and bears; and 
Primates, which includes humans. Eutherian mammals are sometimes 
called placental mammals, because all species have a complex placenta that 
connects a fetus to the mother, allowing for gas, fluid, waste, and nutrient 
exchange. While other mammals may possess a less complex placenta or 
briefly have a placenta, all eutherians have a complex placenta during 
gestation. 


Homeostasis 


"The constant conditions which are maintained in the body might be termed 
equilibria. That word, however, has come to have a fairly exact meaning as 
applied to relatively simple physico-chemical states, in closed systems, 
where known forces are balanced. The coordinated physiological processes 
which maintain most of the steady states in the organism are so complex, 
and so peculiar to living beings - involving, as they may, the brain and 
nerves, the heart, lungs, kidneys and spleen, all working cooperatively - that 
I have suggested a special designation for these states: homeostasis. The 
word does not imply something set and immobile, a stagnation. It means a 
condition - a condition which may vary, but which is relatively constant." 
Walter Cannon, The Wisdom of the Body, 1932, p. 24. 


Cannon was an American physiologist who coined and popularized the 
concept of homeostasis to describe the observations that animals could 
maintain stable internal body conditions even when the external conditions 
changed. Animal organs and organ systems constantly adjust to internal and 
external changes through a process called homeostasis (“steady state”). 
These changes might be in the level of glucose or calcium in blood or in 
external temperatures. Homeostasis means to maintain dynamic 
equilibrium in the body. It is dynamic because it is constantly adjusting to 
the changes that the body’s systems encounter. It is equilibrium because 
body functions are kept within specific ranges. Even an animal that is 
apparently inactive is maintaining this homeostatic equilibrium. 


Homeostatic Process 


The goal of homeostasis is the maintenance of equilibrium around a point 
or value called a set point. While there are normal fluctuations from the set 
point, the body’s systems will usually attempt to go back to this point. A 
change in the internal or external environment is called a stimulus and is 
detected by a receptor; the response of the system is to adjust the parameter 
toward the set point. For instance, if the body becomes too warm, 
adjustments are made to cool the animal. If blood glucose concentration 
rises after a meal, adjustments are made to lower the blood glucose level, 


increasing uptake of glucose from blood into various tissues where it can be 
converted to storage products like glycogen or triglyceride. 


Control of Homeostasis 


When a change occurs in an animal’s environment, an adjustment must be 
made. The receptor senses the change in the environment, then sends a 
signal to the control center (in most cases, the brain) which in turn 
generates a response that is signaled to an effector. The effector is a muscle 
(that contracts or relaxes) or a gland that secretes. Homeostatsis is 
maintained by negative feedback loops. Positive feedback loops actually 
push the organism further out of homeostasis, but may be necessary for life 
to occur. Homeostasis is controlled by the nervous and endocrine system of 
mammals, as described by Cannon in the 1930's. 


Negative Feedback Mechanisms 


Any homeostatic process that changes the direction of the stimulus is a 
negative feedback loop. It can either cause an increase, or a decrease, in 
the level of the stimulus that triggered the response, In all cases the 
response is in the opposite direction of the change in the stimulus. In other 
words, if a level is too high, the body does something to bring it down, and 
conversely, if a level is too low, the body does something to make it go up. 
Hence the term negative feedback. An example is animal maintenance of 
blood glucose levels, as mentioned above. When an animal has eaten, blood 
glucose levels rise. This is sensed by the nervous system. Specialized cells 
in the pancreas sense this, and the hormone insulin is released by the 
endocrine system. Insulin causes blood glucose levels to decrease, as would 
be expected in a negative feedback system, as illustrated in [link]. However, 
if an animal has not eaten and blood glucose levels decrease, this is sensed 
in another group of cells in the pancreas, and the hormone glucagon is 
released, causing glucose levels to increase. This is still a negative feedback 
loop, which is defined as a situation where a change in one direction is 
countered by a response in the opposite direction. Negative feedback loops 
are the predominant mechanism used in homeostasis. 


car & % 


a 
— 
Ts 

rd 


Food is consumed and digested 
In response to the lower causing blood level glucose to rise. In response to higher glucose 
concentration of glucose, the levels, the pancreas secretes 
pancreas stops secreting insulin. insulin into the blood. 


In response to higher insulin levels, 
glucose is transported into cells 
and liver cells store glucose as 


glycogen. As a result, glucose 
levels drop. 


Blood sugar levels are controlled by a negative feedback 
loop. (credit: modification of work by Jon Sullivan) 


Positive Feedback Loop 


A positive feedback loop maintains the direction of the stimulus, possibly 
accelerating it. Few examples of positive feedback loops exist in animal 
bodies, but one is found in the cascade of chemical reactions that result in 
blood clotting, or coagulation. As one clotting factor is activated, it 
activates the next factor in sequence until a fibrin clot is achieved. The 
direction is maintained, not changed, so this is positive feedback. Another 
example of positive feedback is uterine contractions during childbirth, as 
illustrated in [link]. The pituitary hormone oxytocin stimulates the 
contraction of the uterus. This produces pain, which is sensed by the 
nervous system. Instead of lowering the oxytocin and causing the pain to 
subside, the nervous system causes the pituitary to secrete more oxytocin, 
stimulating stronger contractions until the contractions are powerful enough 
to produce childbirth. 


The baby pushes 
against the cervix, 
causing it to stretch. 


Stretching of the 

\ \|) cervix causes 
'// nerve impulses 

to be sent to 

the brain. 


Oxytocin causes le . 2 
the uterus to = ok'= 
contract. 


The brain stimulates 
the pituitary to release 
oxytocin. 


The birth of a human infant 
is the result of positive 
feedback. 


Set Point 


It is possible to adjust a system’s set point, i.e., the level around which the 
parameter of interest fluctuates.. When this happens, the feedback loop 
works to maintain the new setting. An example of this is blood pressure: 
over time, the normal or set point for blood pressure can increase as a result 
of continued increases in blood pressure. The body no longer recognizes the 
elevation as abnormal and no attempt is made to return to the lower set 
point. The result is the maintenance of an elevated blood pressure that can 
have harmful effects on the body. Medication can lower blood pressure and 
lower the set point in the system to a more healthy level. 


Changes can be made in a group of body organ systems in order to maintain 
a set point in another system. This is called acclimatization. This occurs, for 
instance, when an animal migrates to a higher altitude than it is accustomed 
to. In order to adjust to the lower oxygen levels at the new altitude, the body 
increases the number of red blood cells circulating in the blood to ensure 


adequate oxygen delivery to the tissues. Another example of 
acclimatization is animals that have seasonal changes in their coats: a 
heavier coat in the winter ensures adequate heat retention, and a light coat 
in summer assists in keeping body temperature from rising to harmful 
levels. 


Homeostasis: Thermoregulation 


Body temperature affects body activities. Generally, as body temperature 
rises, enzyme activity rises as well. For every ten degree centigrade rise in 
temperature, enzyme activity doubles, up to a point. Body proteins, 
including enzymes, begin to denature and lose their function at even higher 
temperatures, as you learned in a previous module. Enzyme activity will 
also decrease by half for every ten degree centigrade drop in temperature, to 
the point of freezing, with a few exceptions. Some fish can withstand 
freezing solid and return to normal with thawing, and one mammal (the 
Arctic ground squirrel Urocitellus parryii) can lower its body temperature 
to -3° C during its winter hibernation. 


Endotherms and Ectotherms 


Animals can be divided into two groups: some maintain a constant body 
temperature in the face of differing environmental temperatures, while 
others have a body temperature that is the same as their environment, and 
thus varies with the environment. Animals that do not control their body 
temperature are ectotherms. This group has been called cold-blooded, but 
the term may not apply to an animal in the desert with a very warm body 
temperature. In contrast to ectotherms, which rely on external temperatures 
to set their body temperatures, poikilotherms are animals with constantly 
varying internal temperatures. An animal that maintains a constant body 
temperature in the face of environmental changes is called an endotherm. 
Endotherms are animals that rely on internal sources for body temperature 
but which can exhibit extremes in temperature. These animals are able to 
maintain a level of activity at cooler temperature, whereas an ectotherm 
cannot. 


Heat can be exchanged between an animal and its environment through four 
mechanisms: radiation, evaporation, convection, and conduction ((link]). 
Radiation is the emission of electromagnetic “heat” waves. Heat comes 
from the sun in this manner and radiates from dry skin the same way. Heat 
can be removed with liquid from a surface during evaporation. This occurs 
when a Mammal sweats. Convection currents of air remove heat from the 
surface of dry skin as the air passes over it. Heat will be conducted from 
one surface to another during direct contact with the surfaces, such as an 
animal resting on a warm rock. 


(a) Radiation (b) Evaporation 


(c) Convection (d) Conduction 


Heat can be exchanged by four mechanisms: (a) 
radiation, (b) evaporation, (c) convection, or (d) 
conduction. (credit b: modification of work by 
“Kullez”/Flickr; credit c: modification of work by 
Chad Rosenthal; credit d: modification of work by 
“stacey.d”/Flickr) 


Neural Control of Thermoregulation 
The nervous system is important to thermoregulation, as illustrated in 


[link]. The processes of homeostasis and temperature control are centered in 
the hypothalamus of the advanced animal brain. 


Body temperature falls Body temperature rises 


Blood vessels constrict 
so that heat is conserved. 
Sweat glands do not 
secrete fluid. Shivering 


Blood vessels dilate, 
resulting in heat loss to the 
environment. Sweat glands 


secrete fluid. As the fluid 
evaporates, heat is lost 
from the body. 


Normal body 
( temperature 
. . DP XQ Heat is lost to 


The body is able to regulate temperature 
in response to signals from the nervous 
system. 


(involuntary contraction of 
muscles) generates heat, 
which warms the body. 


The hypothalamus maintains the set point for body temperature through 
reflexes that cause vasodilation and sweating when the body is too warm, or 
vasoconstriction and shivering when the body is too cold. It responds to 
chemicals from the body. When a bacterium is destroyed by phagocytic 
leukocytes, chemicals called endogenous pyrogens (pyr=fire and genein=to 
produce) are released into the blood. These chemicals circulate to the 
hypothalamus and reset the thermostat. This allows the body’s temperature 
to increase in what is commonly called a fever. An increase in body 
temperature causes iron to be conserved, inhibiting bacterial division since 
iron is an essential nutrient for bacteria. An increase in body heat also 
increases the activity of the animal’s enzymes and protective cells while 


inhibiting the enzymes and activity of the invading microorganisms. 
Finally, heat itself may also kill the pathogen. Thus, a fever that was once 
thought to be a complication of an infection, is now understood to be a 
normal defense mechanism. 


Digestive Systems 


"If you were to open up a baby's head - and I am not for a moment 
suggesting that you should - you would find nothing but an enormous drool 
gland." - Dave Barry 


The salivary glands (aka "drool glands") of vertebrates are just one part of 
the elaborate and integrated organ system we call the digestive system. The 
digestive system allows organisms, such as us, to obtain their nutrition from 
the consumption of other organisms. Depending on their diet, animals can 
be classified into the following categories: plant eaters (herbivores), meat 
eaters (carnivores), and those that eat both plants and animals (omnivores). 
The nutrients and macromolecules present in food are not immediately 
accessible to the cells. There are a number of processes that modify food 
within the animal body in order to make the nutrients and organic molecules 
accessible for cellular function. As animals evolved in complexity of form 
and function, their digestive systems (including the drool glands) have also 
evolved to accommodate their various dietary needs. 


Herbivores, Omnivores, and Carnivores 


Herbivores are animals whose primary food source is plant-based. 
Examples of herbivores, as shown in [link] include vertebrates like deer, 
koalas, and some bird species, as well as invertebrates such as crickets and 
caterpillars. These animals have evolved digestive systems capable of 
handling large amounts of plant material. Herbivores can be further 
classified into frugivores (fruit-eaters), granivores (seed eaters), nectivores 
(nectar feeders), and folivores (leaf eaters). 


Herbivores, like this (a) American Bison and 
(b) Pipevine Swallowtail caterpillar, eat 
primarily plant material. (photo credit: David 
A. Rintoul) 


Carnivores are animals that eat other animals. The word carnivore is 
derived from Latin and literally means “meat eater.” Wild cats such as lions, 
shown in [link]a and tigers are examples of vertebrate carnivores, as are 
snakes and sharks, while invertebrate carnivores include sea stars, spiders, 
and ladybugs, shown in [link]b. Obligate carnivores are those that rely 
entirely on animal flesh to obtain their nutrients; examples of obligate 
carnivores are members of the cat family, such as lions and cheetahs. 
Facultative carnivores are those that also eat non-animal food in addition to 
animal food. Note that there is no clear line that differentiates facultative 
carnivores from omnivores; dogs would be considered facultative 
carnivores. 


(b) 


Carnivores like the (a) lion eat primarily meat. The 
(b) ambush bug is also a carnivore that consumes 
small insects such as flies. (credit a: modification of 
work by Kevin Pluck; credit b: David A. Rintoul) 


Omnivores are animals that eat both plant- and animal-derived food. In 
Latin, omnivore means to eat everything. Humans, bears (shown in [link]a), 
and chickens are example of vertebrate omnivores; invertebrate omnivores 
include cockroaches and crayfish (shown in [link]b). 


Omnivores like the (a) bear and (b) crayfish eat both 
plant and animal based food. (credit a: modification 
of work by Dave Menke; credit b: modification of 
work by Jon Sullivan) 


Types of Digestive Systems 


There re two types of digestive systems: incomplete and complete. An 
incomplete digestive system has only one opening to the digestive tract 
[link]a. Ingested food and excreted waste products pass through the same 
opening. Incomplete digestive systems are found in Cnidarians and 
Flatworms. The other type is, naturally, called a complete digestive 
system, and this type has two openings [link]b. Food is ingested through 
one opening, and waste products are excreted through a separate opening. 
This type of digestive system is found in all other phyla, including 
vertebrates. 


The advantage of a complete digestive system is that it allows animals to 
feed continuously, without waiting for the residues of the previous meal to 
be released from the digestive tract. It also allows specialization of regions 
of the digestive tract, which means that different food types can be digested 
more efficiently. A particular region along the digestive tract, with different 
physical and chemical conditions, can be optimized for one type of nutrient 
and other regions can be optimized for efficient metabolism of other types 
of nutrients. 


Invertebrate Digestive Systems 


Invertebrates can have incomplete or complete digestive systems, as noted 
above. An incomplete digestive system has a gastrovascular cavity and only 
one opening for digestion. Platyhelminthes (flatworms), Ctenophora (comb 
jellies), and Cnidaria (coral, jelly fish, and sea anemones) have this type of 
digestive system. Gastrovascular cavities, as shown in [link]a, are typically 
a blind tube or cavity with only one opening, the “mouth”, which also 
serves as an “anus”. Ingested material enters the mouth and passes through 
a hollow, tubular cavity. Cells within the cavity secrete digestive enzymes 
that break down the food. The food particles are engulfed by the cells lining 
the gastrovascular cavity. 


A complete digestive system, with an alimentary canal [link]b, is a more 
advanced system: it consists of one tube with a mouth at one end and an 
anus at the other. Earthworms are an example of an animal with a complete 
digestive system. Once the food is ingested through the mouth, it passes 
through the esophagus and is stored in an organ called the crop; then it 
passes into the gizzard where it is churned and digested. From the gizzard, 
the food passes through the intestine, the nutrients are absorbed, and the 
waste is eliminated as feces, called castings, through the anus. 


(a) A gastrovascular cavity has a single opening through 
which food is ingested and waste is excreted, as shown 
in this hydra and in this jellyfish medusa. (b) An 
alimentary canal has two openings: a mouth for ingesting 
food, and an anus for eliminating waste, as shown in this 
nematode. 


Vertebrate Digestive Systems 


Vertebrates have evolved more complex digestive systems to adapt to their 
dietary needs. Some animals have a single stomach, while others have 
multi-chambered stomachs. Birds have developed a digestive system 
adapted to eating unmasticated food. 


Monogastric: Single-chambered Stomach 


As the word monogastric suggests, this type of digestive system consists of 
one (“mono”) stomach chamber (“gastric”). Humans and many animals 
have a monogastric digestive system as illustrated in [link]ab. The process 
of digestion begins with the mouth and the intake of food. The teeth play an 
important role in masticating (chewing) or physically breaking down food 
into smaller particles. The enzymes present in saliva also begin to 
chemically break down food. The esophagus is a long tube that connects the 
mouth to the stomach. Using peristalsis, or wave-like smooth muscle 
contractions, the muscles of the esophagus push the food towards the 
stomach. In order to speed up the actions of enzymes in the stomach, the 
stomach is an extremely acidic environment, with a pH between 1.5 and 
2.5. The gastric juices, which include enzymes in the stomach, act on the 
food particles and continue the process of digestion. Further breakdown of 
food takes place in the small intestine where enzymes produced by the liver, 
the small intestine, and the pancreas continue the process of digestion. The 
nutrients are absorbed into the blood stream across the epithelial cells lining 
the walls of the small intestines. The waste material travels on to the large 
intestine where water is absorbed and the drier waste material is compacted 
into feces; it is stored until it is excreted through the rectum. 


Esophagus 


Liver Stomach Liver 


Stomach 


Pancreas 


Small intestine 


Pancreas Small intestine 


Cecum 


Cecum 


Large intestine 


(a) Human digestive system (b) Rabbit digestive system 


(a) Humans and herbivores, such as the (b) rabbit, have a 
monogastric digestive system. However, in the rabbit the 
small intestine and cecum are enlarged to allow more 
time to digest plant material. The enlarged organ 
provides more surface area for absorption of nutrients. 
Rabbits digest their food twice: the first time food passes 
through the digestive system, it collects in the cecum, 
and then it passes as soft feces called cecotrophes. The 
rabbit re-ingests these cecotrophes to further digest them. 


Avian 


Birds face special challenges when it comes to obtaining nutrition from 
food. Due to the constraints imposed by having to be lightweight in order to 
fly, they have lost some adaptations found in their dinosaur ancestors. For 
example, they do not have teeth, and so their digestive system, shown in 
[link], must be able to process un-masticated food. Birds have evolved a 


variety of beak types that reflect the vast variety in their diet, ranging from 
seeds and insects to fruits and nuts. Because most birds fly, their metabolic 
rates are high in order to efficiently process food and keep their body 
weight low. The stomach of birds has two chambers: the proventriculus, 
where gastric juices are produced to digest the food before it enters the 
stomach, and the gizzard, where the food is stored, soaked, and 
mechanically ground. The undigested material forms food pellets that are 
sometimes regurgitated. Most of the chemical digestion and absorption 
happens in the intestine and the waste is excreted through the cloaca. 


pW 


lie : 


Esophagus 


Crop 


Liver Proventriculus 


Gizzard 
Pancreas 


Small intestine 


Large intestine 


Caeca 


Cloaca 


The avian esophagus has a 
pouch, called a crop, which 
stores food. Food passes from 
the crop to the first of two 


stomachs, called the 
proventriculus, which 
contains digestive juices that 
break down food. From the 
proventriculus, the food 
enters the second stomach, 
called the gizzard, which 
grinds food. Some birds 
swallow stones or grit, which 
are stored in the gizzard, to 
aid the grinding process. 
Birds do not have separate 
openings to excrete urine and 
feces. Instead, uric acid from 
the kidneys is secreted into 
the large intestine and 
combined with waste from 
the digestive process. This 
waste is excreted through an 
opening called the cloaca. 


Note: 

Evolution Connection 

Avian Adaptations 

Birds have a highly efficient, simplified digestive system. Recent fossil 
evidence has shown that the evolutionary divergence of birds from other 
land animals was characterized by streamlining and simplifying the 
digestive system. Unlike many other animals, birds do not have teeth to 
chew their food. In place of lips, they have sharp pointy beaks. Instead of 
teeth, they have a proventricullus, or gizzard, for griding up food. The 
emergence of these changes seems to coincide with the inclusion of seeds 
in the bird diet. Seed-eating birds have beaks that are shaped for grabbing 
seeds and the two-compartment stomach allows for delegation of tasks. 


Since birds need to remain light in order to fly, passage time in the gut is 
very short, which means they digest their food very quickly and need to eat 
often. Contrast this with the ruminants, where the digestion of plant matter 
takes a very long time and a heavy, water-filled digestive tract. What 
would you predict would be some characteristics of birds that eat like a 
cow, ingesting primarily leaves and shoots? 


Ruminants 


Ruminants are herbivores like cows, sheep, goats, bison, etc. whose entire 
diet consists of eating large amounts of leaves and shoots. They have 
evolved digestive systems that help them digest the vast amounts of 
cellulose in this diet. An interesting feature of some ruminants mouths is 
that they do not have upper incisor teeth. They use their lower teeth, tongue 
and lips to tear and chew their food. From the mouth, the food travels to the 
esophagus and on to the stomach. 


To help digest the large amount of plant material, the stomach of the 
ruminants is a multi-chambered organ, as illustrated in [link]. The four 
compartments of the stomach are called the rumen, reticulum, omasum, and 
abomasum. These chambers contain many microbes that break down 
cellulose and ferment ingested food. The abomasum is the “true” stomach 
and is the equivalent of the monogastric stomach chamber where gastric 
juices are secreted. The four-compartment gastric chamber provides a larger 
space and the microbial support necessary to digest plant material in 
ruminants; it is essentially a bacterial fermentation vessel. The fermentation 
process requires lots of watery fluid, and produces large amounts of gas in 
the stomach chamber, which must be eliminated. As in other animals, the 
small intestine plays an important role in nutrient absorption, and the large 
intestine helps in the elimination of waste. 


Large Small 
intestine intestine 


. 


Anus 


a) Reticulum 
a 
fe) u 
masum , J) 


Abomasum , a 


| 


gt 


Ruminant animals, such as goats and cows, have a four 
chambered stomach. The first two chambers, the rumen and 
the reticulum, contain prokaryotes and protists that are able 

to digest cellulose fiber. The ruminant regurgitates cud 

from the reticulum, chews it, and swallows it into a third 
chamber, the omasum, which removes water. The cud then 
passes onto the fourth chamber, the abomasum, where it is 
digested by enzymes produced by the ruminant. 


Parts of the Digestive System 


The vertebrate digestive system is designed to facilitate the transformation 
of food matter into the nutrient components that sustain organisms. 


Oral Cavity 


The oral cavity, or mouth, is the point of entry of food into the digestive 
system, illustrated in [link]. The food consumed is broken into smaller 
particles by mastication, the chewing action of the teeth. All mammals have 
teeth and can chew their food. 


The extensive chemical process of digestion begins in the mouth. As food is 
being chewed, saliva, produced by the salivary glands, mixes with the food. 
Saliva is a watery substance secreted by salivary glands into the mouths of 
many animals. Saliva contains mucus that moistens food and buffers the pH 
of the food. Saliva also contains immunoglobulins and lysozymes, which 
have antibacterial action to reduce tooth decay by inhibiting growth of some 
bacteria. Saliva also contains an enzyme called salivary amylase that begins 
the process of converting starches in the food into a disaccharide called 
maltose. The chewing and wetting action provided by the teeth and saliva 
prepare the food into a mass called the bolus for swallowing. The tongue 
helps in swallowing—moving the bolus from the mouth into the pharynx. 
The pharynx opens to two passageways: the trachea, which leads to the 
lungs, and the esophagus, which leads to the stomach. The trachea has an 
opening called the glottis, which is covered by a cartilaginous flap called 
the epiglottis. When swallowing, the epiglottis closes the glottis and food 
passes into the esophagus and not the trachea. This arrangement allows 
food to be kept out of the trachea and lungs. 


Nasal cavity 


Parotid gland 


Teeth 


Submandibular gland 


Sublingual gland \ 


(a) (b) 


Digestion of food begins in the (a) oral cavity. Food is 
masticated by teeth and moistened by saliva secreted from 
the (b) salivary glands. Enzymes in the saliva begin to 
digest starches and fats. With the help of the tongue, the 
resulting bolus is moved into the esophagus by swallowing. 
(credit: modification of work by the National Cancer 
Institute) 


Esophagus 


The esophagus is a tubular organ that connects the mouth to the stomach. 
The chewed and softened food passes through the esophagus after being 
swallowed. The smooth muscles of the esophagus undergo a series of wave- 
like movements called peristalsis that push the food toward the stomach, as 
illustrated in [link]. The peristalsic wave is unidirectional—it moves food 
from the mouth to the stomach, and reverse movement is not possible. The 
peristaltic movement of the esophagus is an involuntary reflex; it takes 
place in response to the act of swallowing. 


Direction 
of food 


The esophagus transfers food from 


the mouth to the stomach through 
peristaltic movements. 


A ring-like muscle called a sphincter forms valves in the digestive system. 
The gastro-esophageal sphincter is located at the stomach end of the 
esophagus. In response to swallowing and the pressure exerted by the bolus 
of food, this sphincter opens, and the bolus enters the stomach. When there 
is no swallowing action, this sphincter is shut and prevents the contents of 
the stomach from traveling up the esophagus. Many animals have a true 
sphincter; however, in humans, there is no true sphincter, but the esophagus 
remains closed when there is no swallowing action. Acid reflux or 
“heartburn” occurs when the acidic digestive juices escape into the 
esophagus. 


Stomach 


A large part of digestion occurs in the stomach, shown in [link]. The 
stomach is a saclike organ that secretes gastric digestive juices. The pH in 
the stomach is between 1.5 and 2.5. This highly acidic environment is 
required for the chemical breakdown of food and the extraction of nutrients. 
When empty, the stomach is a rather small organ; however, it can expand to 
up to 20 times its resting size when filled with food. This characteristic is 
particularly useful for animals that need to eat when food is available. 


Liver 
Stomach 


Gallbladder 
Pancreas 


Colon 
Transverse colon 
Ascending colon 
Descending colon 


Cecum 


Appendix 


The human stomach has an extremely 
acidic environment where most of the 
protein gets digested. (credit: 
modification of work by Mariana Ruiz 
Villareal) 


The stomach is also the major site for protein digestion in animals other 
than ruminants. Protein digestion is mediated by an enzyme called pepsin in 
the stomach chamber. Pepsin (secreted by cells in the stomach lining) 
breaks peptide bonds and cleaves proteins into smaller polypeptides. 
Another cell type—parietal cells—secrete hydrogen and chloride ions, 
which combine in the lumen to form hydrochloric acid, the primary acidic 
component of the stomach juices. The highly acidic environment also kills 
many microorganisms in the food and, combined with the action of the 
enzyme pepsin, results in the hydrolysis of protein in the food. Chemical 
digestion is facilitated by the churning action of the stomach. Contraction 
and relaxation of smooth muscles completely mixes the stomach contents 
about every 20 minutes. The partially digested food and gastric juice 
mixture is called chyme. Chyme passes from the stomach to the small 
intestine. Further protein digestion takes place in the small intestine. Gastric 
emptying occurs within two to six hours after a meal. Only a small amount 
of chyme is released into the small intestine at a time. The movement of 


chyme from the stomach into the small intestine is regulated by the pyloric 
sphincter. 


When digesting protein and some fats, the stomach lining must be protected 
from getting digested by pepsin. There are two points to consider when 
describing how the stomach lining is protected. Firstly, the enzyme pepsin 
is synthesized in an inactive form (pepsinogen), which is activated by the 
acid and other proteases in the stomach contents. This protects the cells 
which secrete pepsin, because pepsinogen does not have the full enzyme 
functionality of pepsin. Second, the stomach has a thick mucus lining that 
protects the underlying tissue from the action of the digestive juices. When 
this mucus lining is ruptured, ulcers can form in the stomach. Ulcers are 
open wounds in or on an organ caused by bacteria (Helicobacter pylori) 
when the mucus lining is ruptured and fails to reform. 


Small Intestine 


Chyme moves from the stomach to the small intestine. The small intestine 
is the organ where the digestion of protein, fats, and carbohydrates is 
completed. The small intestine is a long tube-like organ with a highly 
folded surface containing finger-like projections called the villi. The apical 
surface of each villus has many microscopic projections called microvilli. 
These structures, illustrated in [link], are lined with epithelial cells on the 
luminal side and allow for the nutrients to be absorbed from the digested 
food and absorbed into the blood stream on the other side. The villi and 
microvilli, with their many folds, increase the surface area of the intestine 
and increase absorption efficiency of the nutrients. Most absorbed nutrients 
(sugars, amino acids and nucleotides) in the blood are carried into the 
hepatic portal vein, which leads to the liver. There, the liver regulates the 
distribution of nutrients to the rest of the body and removes toxic 
substances, including drugs, alcohol, and some pathogens. Fatty acids, 
resulting from digestion of fat in the small intestine, do not enter the blood 
stream directly, but are taken up by the lymphatic system in the small 
intestine. These are eventually delivered to the blood via the thoracic duct, 
to be metabolized by the liver as is the case for the other nutrients. 


Absorptive cells 


Microvilli 


lan = 


Muscle Villi 
layers 


‘ee 


< 4] Fi 7 


j 


y 
* Sn 


Lymphatic vessel 


Villi are folds on the small intestine lining that increase 
the surface area to facilitate the absorption of nutrients. 


The human small intestine is over 6m long and is divided into three parts: 
the duodenum, the jejunum, and the ileum. The “C-shaped,” fixed part of 
the small intestine is called the duodenum and is shown in [link]. The 
duodenum is separated from the stomach by the pyloric sphincter which 
opens to allow chyme to move from the stomach to the duodenum. In the 
duodenum, chyme is mixed with pancreatic juices in an alkaline solution 
rich in bicarbonate that neutralizes the acidity of chyme and acts as a buffer. 
Pancreatic juices also contain several digestive enzymes. Digestive juices 
from the pancreas, liver, and gallbladder, as well as from gland cells of the 
intestinal wall itself, enter the duodenum. Bile is produced in the liver and 
stored and concentrated in the gallbladder. Bile contains bile salts which 
emulsify lipids while the pancreas produces enzymes that catabolize 
starches, disaccharides, proteins, and fats. These digestive juices break 
down the food particles in the chyme into glucose, triglycerides, and amino 
acids. Some chemical digestion of food takes place in the duodenum. 
Absorption of fatty acids into the lymphatic system also takes place in the 
duodenum. 


The second part of the small intestine is called the jejunum, shown in 
[link]. Here, hydrolysis of nutrients is continued while most of the 
carbohydrates and amino acids are absorbed through the intestinal lining. 


The bulk of chemical digestion and nutrient absorption occurs in the 
jejunum. 


The ileum, also illustrated in [link] is the last part of the small intestine and 
here the bile salts and vitamins are absorbed into blood stream. The 
undigested food is sent to the colon from the ileum via peristaltic 
movements of the muscle. The ileum ends and the large intestine begins at 
the ileocecal valve. The vermiform, “worm-like,” appendix is located at the 
ileocecal valve. The appendix of humans secretes no enzymes and has an 
insignificant role in immunity. 


Large Intestine 


The large intestine, illustrated in [link], reabsorbs the water from the 
undigested food material and processes the waste material. The human large 
intestine is much smaller in length compared to the small intestine but 
larger in diameter. It has three parts: the cecum, the colon, and the rectum. 
The cecum joins the ileum to the colon and is the receiving pouch for the 
waste matter. The cecum and colon are home to many trillions of bacteria or 
“intestinal flora” that aid in the digestive processes. The colon can be 
divided into four regions, the ascending colon, the transverse colon, the 
descending colon and the sigmoid colon. The main functions of the colon 
are to extract the water and mineral salts from undigested food, and to store 
waste material. Carnivorous mammals have a shorter large intestine 
compared to herbivorous mammals due to their diet. 


Transverse 
colon 


Ascending 
colon 


Descending 
colon 


Cecum 


Vermiform 


: Sigmoid 
appendix 


colon 
Rectum 


The large intestine reabsorbs water 
from undigested food and stores 
waste material until it is 
eliminated. 


Rectum and Anus 


The rectum is the terminal end of the large intestine, as shown in [link]. 
The primary role of the rectum is to store the feces until defecation. The 
feces are propelled using peristaltic movements during elimination. The 
anus is an opening at the far-end of the digestive tract and is the exit point 
for the waste material. Two sphincters between the rectum and anus control 
elimination: the inner sphincter is involuntary and the outer sphincter is 
voluntary. 


Accessory Organs 


The organs discussed above are the organs of the digestive tract through 
which food passes. Accessory organs are organs that add secretions 
(enzymes) that catabolize food into nutrients. Accessory organs include 
salivary glands, the liver, the pancreas, and the gallbladder. The liver, 


pancreas, and gallbladder are regulated by hormones in response to the food 
consumed. 


The liver is the largest internal organ in humans and it plays a very 
important role in digestion of fats and detoxifying blood. The liver produces 
bile, a digestive juice that is required for the breakdown of fatty 
components of the food in the duodenum. The liver also processes the 
vitamins and fats and synthesizes many plasma proteins. 


The pancreas is another important gland that secretes digestive juices. The 
chyme produced from the stomach is highly acidic in nature; the pancreatic 
juices contain high levels of bicarbonate, an alkali that neutralizes the acidic 
chyme. Additionally, the pancreatic juices contain a large variety of 
enzymes that are required for the digestion of protein and carbohydrates. 


The gallbladder is a small organ that aids the liver by storing bile and 
concentrating bile salts. When chyme containing fatty acids enters the 
duodenum, the bile is secreted from the gallbladder into the duodenum. 


Digestive System Processes 


Introduction 

" Every creature has its own food, and an appropriate alchemist with the task of dividing it ... The 
alchemist takes the food and changes it into a tincture which he sends through the body to become 
blood and flesh. This alchemist dwells in the stomach where he cooks and works. The man eats a 
piece of meat, in which is both bad and good. When the meat reaches the stomach, there is the 
alchemist who divides it. What does not belong to health he casts away to a special place, and 
sends the good wherever it is needed." Philippus Aureolus Paracelsus, in Volumen Medicinae 
Paramirum, c. 1520 


Obtaining nutrition and energy from food is a multi-step process that, contrary to the thinking of 
Paracelsus, does not involve alchemy or an alchemist. Many physical and biochemical processes 
are involved in digestion of food, and it is also a highly regulated process For true animals, the 
first step is ingestion, the act of taking in food. This is followed by digestion, absorption, and 
elimination. In the following sections, each of these steps will be discussed in detail. 


Ingestion 


The large polymeric molecules found in intact food cannot pass through plasma membranes. So 
these polymers need to be broken into smaller monomers so that animal cells can absorb and 
metabolize them to produce energy. The first step in this process is ingestion. Ingestion is the 
process of taking in food through the mouth. In vertebrates, the teeth, saliva, and tongue play 
important roles in mastication (preparing the food into a bolus). While the food is being 
mechanically broken down, the enzymes in saliva begin to chemically process the food as well. 
The combined action of these processes modifies the food from large particles to a soft mass that 
can be swallowed and can travel the length of the esophagus. 


Digestion and Absorption 


Digestion is the mechanical and chemical break down of food into small organic molecules. It is 
important to break down macromolecules into smaller monomers that are of suitable size for 
absorption across the digestive epithelium. Large, complex molecules (e.g., proteins, 
polysaccharides, nucleic acids, and lipids) must be hydrolyzed into monomers before they can be 
absorbed by the digestive epithelial cells. If this terminology seems a bit crazy, you may want to 
review hydrolysis reactions [link] before proceeding. Different organs play specific roles in the 
digestive process. The animal diet needs carbohydrates, protein, nucleic acids, and fat, as well as 
vitamins and inorganic components for nutritional balance. We will briefly discuss digestion and 
absorption of some of these in the sections below. 


Carbohydrates 


The digestion of carbohydrates begins in the mouth. The salivary enzyme amylase begins the 
breakdown of food starches into maltose, a disaccharide. No significant further digestion of 
carbohydrates takes place in the stomach. The esophagus produces no digestive enzymes but does 


produce mucous for lubrication. The acidic environment in the stomach inhibits the action of the 
salivary amylase enzyme. 


The next step of carbohydrate digestion takes place in the duodenum. The chyme from the 
stomach enters the duodenum and mixes with the digestive secretions from the pancreas, liver, 
and gallbladder. Pancreatic juices also contain an amylase enzyme, which continues the 
breakdown of starch and glycogen into maltose, a disaccharide. The disaccharides are broken 
down into monosaccharides by enzymes called maltases, sucrases, and lactases, which are also 
present in cells lining the small intestine. Maltase breaks down maltose into glucose. Other 
disaccharides, such as sucrose and lactose are broken down by sucrase and lactase, respectively. 
Sucrase breaks down sucrose (or “table sugar”) into glucose and fructose, and lactase breaks 
down lactose (or “milk sugar’) into glucose and galactose. The monosaccharides (e.g., glucose 
and fructose) thus produced are absorbed by the intestinal cells and transported into the 
bloodstream. The steps in carbohydrate digestion are summarized in [link] and [link]. 


Polysaccharides 
Amylase 
Disaccharides 


Maltase Sucrase Lactase 


Monosaccharides Glucose + fructose Glucose + galactose 


Digestion of carbohydrates is performed by several 
enzymes. Starch and glycogen are broken down into glucose 
by amylase and maltase. Sucrose (table sugar) and lactose 
(milk sugar) are broken down by sucrase and lactase, 
respectively. 


me 


Digestion of Carbohydrates 


Produced Site of Substrate 
Enzyme By Action Acting On End Products 
Salivary amylase Sallvary Mouth Poly a onanies aul 
er glands (Starch) s 


oligosaccharides 


Digestion of Carbohydrates 


Produced Site of Substrate 

Enzyme By Action Acting On End Products 

: Small Polysaccharides Disacchonaes 
Pancreatic amylase Pancreas ' . (maltose), 
intestine (starch) : 
monosaccharides 

Lining of 
the Monosaccharides 

Oligosaccharidases ESUNE: lon Disaccharides (e.g., glucose, 
brush intestine fructose, 
border galactose) 
membrane 

Protein 


A large part of protein digestion takes place in the stomach. The enzyme pepsin plays an 
important role in the digestion of proteins by breaking down the intact protein to peptides, which 
are short chains of four to nine amino acids. In the duodenum, other enzymes—trypsin, elastase, 
and chymotrypsin—act on the peptides reducing them to smaller peptides. Trypsin elastase, 
carboxypeptidase, and chymotrypsin are produced by the pancreas and released into the 
duodenum where they act on the chyme. Further breakdown of peptides to single amino acids is 
aided by enzymes called peptidases (those that break down peptides). Specifically, 
carboxypeptidase, dipeptidase, and aminopeptidase play important roles in reducing the peptides 
to free amino acids. The amino acids are absorbed into the bloodstream through the small 
intestines. The steps in protein digestion are summarized in [link] and [link]. 


The liver regulates 
distribution of 
amino acids to the 
rest of the body. 


In the stomach, 
pepsin breaks 
down proteins 
into fragments, 


called peptides. 


Amino acids are 
absorbed from the 
small intestine into 
the blood stream. 


Protein-digesting 
enzymes are 
secreted from 
the pancreas 
into the small 
intestine. 


In the small 
intestine, a variety 
of enzymes break 


large peptides 
Asmall amount into smaller 
of dietary protein peptides, and then 
is lost in the feces. into individual 


amino acids. 
Protein digestion is a multistep process that 


begins in the stomach and continues through 
the intestines. 


Digestion of Protein 


Produced Site of 
Enzyme By Action 
Pepsin ae Stomach 


chief cells 


Trypsin 
Elastase Pancreas 
Chymotrypsin 


Small 
intestine 


Substrate 

Acting On End Products 
Proteins Peptides 
Proteins Peptides 


Digestion of Protein 


Produced Site of Substrate 
Enzyme By Action Acting On End Products 
' Small : Amino acids 
Carboxypeptidase Pancreas iramotiae Peptides andl peptides 
Pope pase pulls . sila Peptides Amino acids 
Dipeptidase intestine intestine 


Lipids 


The bulk of lipid digestion occurs in the small intestine, via the action of pancreatic lipase. When 
chyme enters the duodenum, it triggers a hormonal response resulting in the release of bile, which 
is produced in the liver and stored in the gallbladder. Bile aids in the digestion of lipids, primarily 
triglycerides, by emulsification. Emulsification is a physical process in which large lipid globules 
are dispersed into several small lipid globules. Lipids are hydrophobic substances: in the presence 
of water, they will aggregate to form large globules to minimize exposure to water. These small 
globules have a larger surface-to-volume ratio and thus an increased surface area for the lipases to 
interact with. Bile contains bile salts, which are amphipathic, meaning they contain hydrophobic 
and hydrophilic parts. Thus, the bile salts hydrophilic side can interface with water on one side 
and the hydrophobic side interfaces with lipids on the other. By doing so, bile salts emulsify large 
lipid globules into small lipid globules. 


By forming an emulsion, bile salts increase the available surface area of the lipid particles 
significantly. The pancreatic lipases can then act on the lipids more efficiently and digest them, as 
detailed in [link]. Lipases break down the dietary triglycerides into fatty acids and monoglycerides 
(one fatty acid attached to a glycerol molecule). These molecules can pass through the plasma 
membrane of the cell and enter the epithelial cells of the intestinal lining. Lipase products (fatty 
acids and monoglycerides) pass through the intestinal cells where they are reassembled into 
triglycerides, and then are combined with proteins to form large fatty complexes called 
chylomicrons. Chylomicrons contain triglycerides, cholesterol, and other lipids and have proteins 
on their surface. The surface is also composed of the hydrophilic phosphate "heads" of 
phospholipids. Together, they enable the chylomicron to move in an aqueous environment without 
exposing the lipids to water. Chylomicrons leave the absorptive cells via exocytosis. 
Chylomicrons enter the lymphatic vessels, and then enter the blood via the thoracic duct on their 
way to the liver. 


1. Lipids are emulsified 
by the bile. 


<a 
muision 


Lumen of XE 


intestine 

ag 3 
Absorptive X% 74 
epithelial cell i 


Lymphatic 
capillary 


(a) 


2. 


Lipases break 
down triglycerides 
into fatty acids and 
monoglycerides. 


Fatty acids and 
monoglycerides 
are packaged into 
micelles that are 
absorbed by 
microvilli. 


. Fatty acids and 


monoglycerides 
are converted 
back into 
triglycerides. 

The triglycerides 
aggregate with 
cholesterol, 
proteins, and 
phospholipids to 
form chylomicrons. 


. The chylomicrons 


move into a lymph 
capillary, which 
transports them to 
the rest of the body. 


Triglyceride (fat) 


Monoglyceride 


Lipase 


+ 


(b) 


Lipids are digested and absorbed in the small intestine. 


Summary of Digestion 


+ Mechanical digestion (chewing 
and swallowing) 

* Chemical digestion of 
carbohydrates 


* Mechanical digestion (peristaltic 
mixing and propulsion) 

+ Chemical digestion of proteins 

+ Absorption of lipid-soluble 
substances, such as aspirin 


Esophagus 


Liver 


Gallbladder ; ; . ici 
* Mechanical digestion (mixing 


y and propulsion, primarily 
Pylorus g by segmentation) 

* Chemical digestion of 
carbohydrates, lipids, proteins, 
and nucleic acids 

* Absorption of peptides, amino 
acids, glucose, fructose, lipids, 
water, minerals, and vitamins 


Pancreas 


+ Mechanical digestion 
(segmental mixing, mass 
movement for propulsion) 

* No chemical digestion except 
by bacteria 

+ Absorption of ions, water, 
minerals, vitamins, and small 
organic molecules produced 
by bacteria 


Rectum 


Anal sphincters 


Mechanical and chemical digestion of 
food takes place in many steps, beginning 
in the mouth and ending in the rectum. 


Elimination 


The final step in digestion is the elimination of undigested food content and waste products. The 
undigested food material enters the colon, where most of the water is reabsorbed. Recall that the 
colon is also home to the microflora called “intestinal flora” that aid in the digestion process. The 
semi-solid waste is moved through the colon by peristaltic movements of the muscle and is stored 
in the rectum. As the rectum expands in response to storage of fecal matter, it triggers the neural 
signals required to set up the urge to eliminate. The solid waste is eliminated through the anus 


using peristaltic movements of the rectum. 


Nutrition 


"Tell me what you eat: I will tell you what you are." Jean-Anthelme Brillat- 
Savarin, The Philosopher in the Kitchen, Aphorism IV, 1825 


Brillat-Savarin's aphorism may not be entirely true, but it holds a grain of 
truth. Given the diversity of animal life on our planet, it is not surprising that 
the animal diet would also vary substantially. The animal diet is the source of 
materials needed for building DNA and other complex molecules needed for 
growth, maintenance, and reproduction; collectively these processes are 
called biosynthesis. The diet is also the source of materials for ATP 
production in the cells. The diet must be balanced to provide the minerals and 
vitamins that are required for cellular function. 


Food Requirements 


What are the fundamental requirements of the animal diet? The animal diet 
should be well balanced and provide nutrients required for bodily function 
and the minerals and vitamins required for maintaining structure and 
regulation necessary for good health and reproductive capability. These 
requirements for a human are illustrated graphically in [link] 


Vegetables ry 


Choose Ov 


For humans, a balanced diet 


includes fruits, vegetables, 
grains, and protein. (credit: 
USDA) 


Note: 

Everyday Connection 

Let’s Move! Campaign 

Obesity is a growing epidemic and the rate of obesity among children is 
rapidly rising in the United States. To combat childhood obesity and ensure 
that children get a healthy start in life, first lady Michelle Obama has 
launched the Let’s Move! campaign. The goal of this campaign is to educate 
parents and caregivers on providing healthy nutrition and encouraging active 
lifestyles to future generations. This program aims to involve the entire 
community, including parents, teachers, and healthcare providers to ensure 
that children have access to healthy foods—more fruits, vegetables, and 
whole grains—and consume fewer calories from processed foods. Another 
goal is to ensure that children get physical activity. With the increase in 
television viewing and stationary pursuits such as video games, sedentary 
lifestyles have become the norm. Learn more at www.letsmove.gov. 


Organic Precursors 


The organic molecules required for building cellular material and tissues must 
come from food. Carbohydrates or sugars are the primary source of organic 
carbons in the animal body. During digestion, digestible carbohydrates are 
ultimately broken down into glucose and used to provide energy through 
metabolic pathways. Complex carbohydrates, including polysaccharides, can 
be broken down into glucose through biochemical modification; however, 
humans do not produce the enzyme cellulase and lack the ability to derive 
glucose from the polysaccharide cellulose. In humans, these molecules 
provide the fiber required for moving waste through the large intestine and a 
healthy colon. The intestinal flora in the human gut are able to extract some 


nutrition from these plant fibers. The excess sugars in the body are converted 
into glycogen and stored in the liver and muscles for later use. Glycogen 
stores are used to fuel prolonged exertions, such as long-distance running, 
and to provide energy during food shortage. Excess glycogen can be 
converted to fats, which are stored in the lower layer of the skin of mammals 
for insulation and energy storage. Excess digestible carbohydrates are stored 
by mammals in order to survive famine and aid in mobility. 


Another important requirement is that of nitrogen. Protein catabolism 
provides a source of organic nitrogen. Amino acids are the building blocks of 
proteins and protein breakdown provides amino acids that are used for 
cellular function. The carbon and nitrogen derived from these become the 
building block for nucleotides, nucleic acids, proteins, cells, and tissues. 
Excess nitrogen must be excreted as it is toxic. Fats add flavor to food and 
promote a sense of satiety or fullness. Fatty foods are also significant sources 
of energy because one gram of fat contains nine calories. Fats are required in 
the diet to aid the absorption of fat-soluble vitamins and the production of fat- 
soluble hormones. 


Essential Nutrients 


While the animal body can synthesize many of the molecules required for 
function from the organic precursors, there are some nutrients that need to be 
consumed from food. These nutrients are termed essential nutrients, 
meaning they must be eaten, and the body cannot produce them. 


The omega-3 alpha-linolenic acid and the omega-6 linoleic acid are essential 
fatty acids needed to make some membrane phospholipids. Vitamins are 
another class of essential organic molecules that are required in small 
quantities for many enzymes to function and, for this reason, are considered 
to be co-enzymes. Absence or low levels of vitamins can have a dramatic 
effect on health, as outlined in [link] and [link]. Both fat-soluble and water- 
soluble vitamins must be obtained from food. Minerals, listed in [link], are 
inorganic essential nutrients that must be obtained from food. Among their 
many functions, minerals help in structure and regulation and are considered 
co-factors. Certain amino acids also must be procured from food and cannot 
be synthesized by the body. These amino acids are the “essential” amino 


acids. The human body can synthesize only 11 of the 20 required amino 
acids; the rest must be obtained from food. The essential amino acids are 


listed in [link]. 


Water-soluble Essential Vitamins 


Vitamin 


Vitamin By, 
(Thiamine) 


Vitamin Bo 
(Riboflavin) 


Function 


Needed by the 
body to process 
lipids, proteins, 
and 
carbohydrates 
Coenzyme 
removes CO> 
from organic 
compounds 


Takes an active 
role in 
metabolism, 
aiding in the 
conversion of 
food to energy 
(FAD and 
FMN) 


Deficiencies 
Can Lead To 


Muscle 
weakness, 
Beriberi: 
reduced heart 
function, CNS 
problems 


Cracks or sores 
on the outer 
surface of the 
lips (cheliosis); 
inflammation 
and redness of 
the tongue; 
moist, scaly 
skin 
inflammation 
(seborrheic 
dermatitis) 


Sources 


Milk, 
meat, dried 
beans, 
whole 
grains 


Meat, 
eggs, 
enriched 
grains, 
vegetables 


Water-soluble Essential Vitamins 


Vitamin 


Vitamin Bz 
(Niacin) 


Vitamin Bs 
(Pantothenic 
acid) 


Vitamin Bg 
(Pyridoxine) 


Function 


Used by the 
body to release 
energy from 
carbohydrates 
and to process 
alcohol; 
required for the 
synthesis of sex 
hormones; 
component of 
coenzyme 
NAD* and 
NADP* 


Assists in 
producing 
energy from 
foods (lipids, in 
particular); 
component of 
coenzyme A 


The principal 
vitamin for 
processing 
amino acids 
and lipids; also 
helps convert 
nutrients into 
energy 


Deficiencies 
Can Lead To 


Pellagra, which 
can result in 
dermatitis, 
diarrhea, 
dementia, and 
death 


Fatigue, poor 
coordination, 
retarded 
growth, 
numbness, 
tingling of 
hands and feet 


Irritability, 
depression, 
confusion, 
mouth sores or 
ulcers, anemia, 
muscular 
twitching 


Sources 


Meat, 
eggs, 
grains, 
nuts, 
potatoes 


Meat, 
whole 
grains, 
milk, 
fruits, 
vegetables 


Meat, 
dairy 
products, 
whole 
grains, 
orange 
juice 


Water-soluble Essential Vitamins 


Vitamin 


Vitamin B7 


(Biotin) 


Vitamin Bo 
(Folic acid) 


Vitamin B 12 
(Cobalamin) 


Function 


Used in energy 
and amino acid 
metabolism, fat 
synthesis, and 
fat breakdown; 
helps the body 
use blood sugar 


Assists the 
normal 
development of 
cells, especially 
during fetal 
development; 
helps 
metabolize 
nucleic and 
amino acids 


Maintains 
healthy nervous 
system and 
assists with 
blood cell 
formation; 
coenzyme in 
nucleic acid 
metabolism 


Deficiencies 
Can Lead To 


Hair loss, 
dermatitis, 
depression, 
numbness and 
tingling in the 
extremities; 
neuromuscular 
disorders 


Deficiency 
during 
pregnancy is 
associated with 
birth defects, 
such as neural 
tube defects 
and anemia 


Anemia, 
neurological 
disorders, 
numbness, loss 
of balance 


Sources 


Meat, 
eggs, 
legumes 
and other 
vegetables 


Leafy 
green 
vegetables, 
whole 
wheat, 
fruits, 

nuts, 
legumes 


Meat, 
eggs, 
animal 
products 


Water-soluble Essential Vitamins 


Deficiencies 
Vitamin Function Can Lead To Sources 


ee rvy, which 
Helps maintain eet y Citrus 
results in 


connective fruits, 
bleeding, hair 


Vitamin C tissue: bone, Sa Aon isc broccoli, 
(Ascorbic cartilage, and ° : pas ‘ tomatoes, 
acid) dentin; boosts om Yee and red sweet 
the maine swelling; bell 
Lee res delayed wound eee 
y healing PEPP 
Fat-soluble Essential Vitamins 
Deficiencies 
Can Lead 


Vitamin Function To Sources 


Fat-soluble Essential Vitamins 


Vitamin 


Vitamin A 
(Retinol) 


Vitamin D 


Function 


Critical to the 
development 
of bones, 
teeth, and 
skin; helps 
maintain 
eyesight, 
enhances the 
immune 
system, fetal 
development, 
gene 
expression 


Critical for 
calcium 
absorption for 
bone 
development 
and strength; 
maintains a 
stable nervous 
system; 
maintains a 
normal and 
strong 
heartbeat; 
helps in blood 
clotting 


Deficiencies 
Can Lead 
To 


Night- 
blindness, 
skin 
disorders, 
impaired 
immunity 


Rickets, 


osteomalacia, 


immunity 


Sources 


Dark green 
leafy 
vegetables, 
yellow- 
orange 
vegetables 
fruits, 
milk, 
butter 


Cod liver 
oil, milk, 
egg yolk 


Fat-soluble Essential Vitamins 


Vitamin 


Vitamin E 
(Tocopherol) 


Vitamin K 
(Phylloquinone) 


A healthy diet should include a variety of 


Function 


Lessens 
oxidative 
damage of 
cells,and 
prevents lung 
damage from 
pollutants; 
vital to the 
immune 
system 


Essential to 
blood clotting 


Deficiencies 
Can Lead 
To 


Deficiency is 
rare; anemia, 
nervous 
system 
degeneration 


Bleeding and 
easy bruising 


Sources 


Wheat 
germ oil, 
unrefined 
vegetable 
oils, nuts, 
seeds, 
grains 


Leafy 
green 
vegetables, 
tea 


foods to ensure that needs for essential 
nutrients are met. (credit: Keith Weller, 
USDA ARS) 


Minerals and Their Function in the Human Body 


Mineral 


*Calcium 


* Chlorine 


Function 


Needed for 
muscle and 
neuron function; 
heart health; 
builds bone and 
supports 
synthesis and 
function of blood 
cells; nerve 
function 


Needed for 
production of 
hydrochloric acid 
(HC]) in the 
stomach and 
nerve function; 
osmotic balance 


Deficiencies 
Can Lead To 


Osteoporosis, 
rickets, 
muscle 
spasms, 
impaired 
growth 


Muscle 
cramps, mood 
disturbances, 
reduced 
appetite 


Sources 


Milk, 
yogurt, 
fish, green 
leafy 
vegetables, 
legumes 


Table salt 


Minerals and Their Function in the Human Body 


Mineral 


Copper 
(trace 
amounts) 


Iodine 


Iron 


Function 


Required 
component of 
many redox 
enzymes, 
including 
cytochrome c 
oxidase; cofactor 
for hemoglobin 
synthesis 


Required for the 
synthesis of 
thyroid hormones 


Required for 
many proteins 
and enzymes, 
notably 
hemoglobin, to 
prevent anemia 


Deficiencies 
Can Lead To 


Copper 
deficiency is 
rare 


Goiter 


Anemia, 
which causes 
poor 
concentration, 
fatigue, and 
poor immune 
function 


Sources 


Liver, 
oysters, 
cocoa, 
chocolate, 
sesame, 
nuts 


Seafood, 
iodized 
salt, dairy 
products 


Red meat, 
leafy green 
vegetables, 
fish (tuna, 
salmon), 
eggs, dried 
fruits, 
beans, 
whole 
grains 


Minerals and Their Function in the Human Body 


Mineral 


*Magnesium 


Manganese 
(trace 
amounts) 


Molybdenum 
(trace 
amounts) 


*Phosphorus 


Function 


Required co- 
factor for ATP 


formation; bone 


formation; 
normal 
membrane 


functions; muscle 


function 


A cofactor in 
enzyme 
functions; trace 
amounts are 
required 


Acts as a cofactor 
for three essential 


enzymes in 
humans: sulfite 


oxidase, xanthine 


oxidase, and 


aldehyde oxidase 


A component of 
bones and teeth; 


helps regulate 
acid-base 
balance; 
nucleotide 
synthesis 


Deficiencies 
Can Lead To 


Mood 
disturbances, 
muscle 
spasms 


Manganese 
deficiency is 
rare 


Molybdenum 
deficiency is 
rare 


Weakness, 
bone 
abnormalities, 
calcium loss 


Sources 


Whole 
grains, 
leafy green 
vegetables 


Common 
in most 
foods 


Milk, hard 
cheese, 
whole 
grains, 
meats 


Minerals and Their Function in the Human Body 


Mineral 


*Potassium 


Selenium 
(trace 
amounts) 


*Sodium 


Zinc (trace 


amounts) 


Function 


Vital for muscles, 
heart, and nerve 
function 


A cofactor 
essential to 
activity of 
antioxidant 
enzymes like 
glutathione 
peroxidase; trace 
amounts are 
required 


Systemic 
electrolyte 
required for many 
functions; acid- 
base balance; 
water balance; 
nerve function 


Required for 
several enzymes 
such as 
carboxypeptidase, 
liver alcohol 
dehydrogenase, 
and carbonic 
anhydrase 


Deficiencies 
Can Lead To 


Cardiac 
rhythm 
disturbance, 
muscle 
weakness 


Selenium 
deficiency is 
rare 


Muscle 
cramps, 
fatigue, 
reduced 
appetite 


Anemia, poor 
wound 
healing, can 
lead to short 
stature 


Sources 


Legumes, 
potato 
skin, 
tomatoes, 
bananas 


Common 
in most 
foods 


Table salt 


Common 
in most 
foods 


Minerals and Their Function in the Human Body 


Deficiencies 
Mineral Function Can Lead To Sources 
*Greater than 200mg/day required 
Essential Amino Acids 
Amino acids that must be Amino acids anabolized by the 
consumed body 
isoleucine alanine 
leucine selenocysteine 
lysine aspartate 
methionine cysteine 
phenylalanine glutamate 
tryptophan glycine 
valine proline 
histidine* serine 
threonine tyrosine 


arginine* asparagine 


Essential Amino Acids 


Amino acids that must be Amino acids anabolized by the 
consumed body 


*The human body can synthesize histidine and arginine, but not in the 
quantities required, especially for growing children. 


The Circulatory System 


Introduction 

"Observation by means of the microscope will reveal more wonderful 
things than those viewed in regard to mere structure and connection: for 
while the heart is still beating the contrary (i.e., in opposite directions in the 
different vessels) movement of the blood is observed in the vessels—though 
with difficulty—so that the circulation of the blood is clearly exposed." 
Marcello Malpighi, De Pulmonibus, 1661 


Malpighi's work (mostly on frogs) outlined the finer microscopic details of 
circulation, following the work of Harvey, who described the circulatory 
system at a macroscopic level. In all animals, except a few simple types, the 
circulatory system is used to transport nutrients and gases through the body. 
Simple diffusion allows some water, nutrient, waste, and gas exchange into 
primitive animals that are only a few cell layers thick; however, bulk flow is 
the only method by which the entire body of larger more complex 
organisms is accessed. 


Circulatory System Architecture 


The circulatory system is effectively a network of cylindrical vessels: the 
arteries, veins, and capillaries that emanate from a pump, the heart. In all 
vertebrate organisms, as well as some invertebrates, this is a closed system, 
in which the blood is not free in a cavity. In a closed circulatory system, 
blood is contained inside blood vessels and circulates unidirectionally from 
the heart around the systemic circulatory route, then returns to the heart 
again, as illustrated in [link]a. As opposed to a closed system, arthropods— 
including insects, crustaceans, and most mollusks—have an open 
circulatory system, as illustrated in [link]b. In an open circulatory system, 
the fluid is not enclosed in the blood vessels but is pumped into a cavity 
called a hemocoel; rather than blood, this fluid is called hemolymph 
because the blood mixes with the interstitial fluid. As the heart beats and 
the animal moves, the hemolymph circulates around the organs within the 
body cavity and then reenters the hearts through openings called ostia. This 
movement allows for gas and nutrient exchange. An open circulatory 
system does not use as much energy as a closed system to operate or to 


maintain; however, there is a trade-off with the amount of blood that can be 
moved to highly metabolically active organs and tissues. 


Dorsal blood vessel Hearts Ostia (openings in heart) 
(main heart) : 


Dorsal blood 
vessel 


Body cavity 


Ventral blood vessel 


(a) Closed circulatory system (b) Open circulatory system 


In (a) closed circulatory systems, the heart pumps blood through 
vessels that are separate from the interstitial fluid of the body. 
Most vertebrates and some invertebrates, like this annelid 
earthworm, have a closed circulatory system. In (b) open 
circulatory systems, a fluid called hemolymph is pumped through 
a blood vessel that empties into the body cavity. Hemolymph 
returns to the blood vessel through openings called ostia. 
Arthropods like this bee and most mollusks have open circulatory 
systems. 


Circulatory System Variation in Animals 


The circulatory system varies from simple systems in invertebrates to more 
complex systems in vertebrates. The simplest animals, such as the sponges 
(Porifera) and rotifers (Rotifera), do not need a circulatory system because 
diffusion allows adequate exchange of water, nutrients, and waste, as well 
as dissolved gases, as shown in [link]a. Organisms that are more complex 
but still only have two layers of cells in their body plan, such as jellies 
(Cnidaria) and comb jellies (Ctenophora) also use diffusion through their 
epidermis and internally through the gastrovascular compartment. Both 


their internal and external tissues are bathed in an aqueous environment and 
exchange fluids by diffusion on both sides, as illustrated in [link]b. 
Exchange of fluids is assisted by the pulsing of the jellyfish body. 


(a) Sponge (b) Jellyfish 


Simple animals consisting of a single cell layer such as the (a) 
sponge or only a few cell layers such as the (b) jellyfish do not 
have a circulatory system. Instead, gases, nutrients, and wastes are 
exchanged by diffusion. 


For more complex organisms, diffusion is not efficient for moving gases, 
nutrients, and waste effectively through the body; natural selection led to 
the development of more efficient systems. Most arthropods and many 
mollusks have open circulatory systems. In an open system, an elongated 
beating heart pushes the hemolymph through the body, and muscle 
contractions help to move fluids. The larger more complex crustaceans, 
including lobsters, have developed arterial-like vessels to push blood 
through their bodies, and the most active mollusks, such as squids, have 
evolved a closed circulatory system and are able to move rapidly to catch 
prey. Closed circulatory systems are found in all vertebrates; however, there 


are significant differences in the structure of the heart and the circulation of 
blood between the different vertebrate groups due to adaptation during 
evolution and associated differences in anatomy. [link] illustrates the basic 
circulatory systems of some vertebrates: fish, amphibians, reptiles, and 
mammals. 


Gill circulation 


Gill 
capillaries 


Ventricle 


Body 
Systemic circulation capillaries 


(a) Fish 


Pulmonary circulation 


Lung 
capillaries 


Left 


atrium 
= Septum 
atrium 
Right Left 
ventricle ventricle 


Body 
capillaries 


Systemic circulation 


(c) Reptile 


Pulmonary and 
skin circulation 


Lung and 
skin capillaries 


Right atrium Left atrium 


Body capillaries Ventricle 


Systemic circulation 
(b) Amphibians 


Pulmonary circulation 


Left atrium 


Lung 
capillaries 


Body capillaries 


Right Ei 4Aev See Left 
ventricle =< = ventricle 


Systemic circulation 
(d) Mammals 


(a) Fish have the simplest circulatory systems of the vertebrates: 
blood flows unidirectionally from the two-chambered heart 
through the gills and then the rest of the body. (b) Amphibians 
have two circulatory routes: one for oxygenation of the blood 
through the lungs and skin, and the other to take oxygen to the rest 
of the body. The blood is pumped from a three-chambered heart 


with two atria and a single ventricle. (c) Reptiles also have two 
circulatory routes; however, blood is only oxygenated through the 
lungs. The heart is three chambered, but the ventricles are partially 
separated so some mixing of oxygenated and deoxygenated blood 
occurs except in crocodilians and birds. (d) Mammals and birds 
have the most efficient heart with four chambers that completely 
separate the oxygenated and deoxygenated blood; it pumps only 
oxygenated blood through the body and deoxygenated blood to the 
lungs. 


As illustrated in [link]a Fish have a single circuit for blood flow and a two- 
chambered heart that has only a single atrium and a single ventricle. The 
atrium collects blood that has returned from the body, and the ventricle 
pumps the blood to the gills where gas exchange occurs and the blood is re- 
oxygenated; this is called the gill circulation. The blood then continues 
through the rest of the body before arriving back at the atrium; this is called 
the systemic circulation. This unidirectional flow of blood produces a 
gradient of oxygenated to deoxygenated blood around the fish’s systemic 
circuit. The result is a limit in the amount of oxygen that can reach some of 
the organs and tissues of the body, reducing the overall metabolic capacity 
of fish. 


In amphibians, reptiles, birds, and mammals, blood flow is directed in two 
circuits: one through the lungs and back to the heart, which is called the 
pulmonary circulation, and the other throughout the rest of the body and 
its organs including the brain (systemic circulation). In amphibians, gas 
exchange also occurs through the skin during pulmonary circulation and is 
referred to as pulmocutaneous circulation. 


As shown in [link]b, amphibians have a three-chambered heart that has two 
atria and one ventricle rather than the two-chambered heart of fish. The two 
atria (superior heart chambers) receive blood from the two different circuits 
(the lungs and the systems), and then there is some mixing of the blood in 
the heart’s ventricle (inferior heart chamber), which reduces the oxygen 
concentration in the blood pumped from the ventricle. The advantage to this 


arrangement is that high pressure in the vessels pushes blood to the lungs 
and body. The mixing is mitigated by a ridge within the ventricle that 
diverts oxygen-rich blood through the systemic circulatory system and 
deoxygenated blood to the pulmocutaneous circuit. For this reason, 
amphibians are often described as having double circulation. 


Most reptiles also have a three-chambered heart similar to the amphibian 
heart that directs blood to the pulmonary and systemic circuits, as shown in 
[link]c. The ventricle is divided more effectively by a partial septum, which 
results in even less mixing of oxygenated and deoxygenated blood. Some 
reptiles (alligators and crocodiles) are the most primitive animals to exhibit 
a four-chambered heart. Crocodilians have a unique circulatory mechanism 
where the heart shunts blood from the lungs toward the stomach and other 
organs during long periods of submergence, for instance, while the animal 
waits for prey or stays underwater waiting for prey to rot. One adaptation 
includes two main arteries that leave the same part of the heart: one takes 
blood to the lungs and the other provides an alternate route to the stomach 
and other parts of the body. Two other adaptations include a hole in the 
heart between the two ventricles, called the foramen of Panizza, which 
allows blood to move from one side of the heart to the other, and 
specialized connective tissue that slows the blood flow to the lungs. 
Together these adaptations have made crocodiles and alligators one of the 
most successful and ancient animal groups on earth. 


In mammals and birds, the heart is also divided into four chambers: two 
atria and two ventricles, as illustrated in [link]d. The oxygenated blood is 
completely separated from the deoxygenated blood, which improves the 
efficiency of double circulation and is probably required for the warm- 
blooded lifestyle of mammals and birds. The four-chambered heart of birds 
and mammals evolved independently from ancestors with a three- 
chambered heart. The independent evolution of the same or a similar 
biological trait is referred to as convergent evolution. 


Components of Blood 


Oxygen-binding proteins (hemoglobin, hemocyanin, etc.) are one of the 
main components of blood in all animals. The blood is more than those 


proteins, though. Blood is actually a term used to describe the liquid that 
moves through the vessels and includes plasma (the liquid portion, which 
contains water, proteins, salts, lipids, and glucose) and the cells (red and 
white cells) and cell fragments called platelets. Plasma is actually the major 
component of blood and contains the water, proteins, electrolytes, lipids, 
and glucose. The cells are responsible for carrying the gases (red cells) and 
immune the response (white). The platelets are responsible for blood 
clotting. In humans, cellular components make up approximately 45 percent 
of the blood and the liquid plasma 55 percent. Blood is 20 percent of a 
human's extracellular fluid and eight percent of the weight of an average 
human. 


The Role of Blood in the Body 


Blood, like the human blood illustrated in [link] is important for regulation 
of the body’s systems and homeostasis. Blood helps maintain homeostasis 
by stabilizing pH, temperature, osmotic pressure, and by eliminating excess 
heat. Blood supports growth by distributing nutrients and hormones, and by 
removing waste. Blood plays a protective role by transporting clotting 
factors and platelets to prevent blood loss and transporting the disease- 
fighting agents or white blood cells to sites of infection. 


— Monocyte 


Erythrocyte 
en blood “| 


Eosinophil ; = A 
¥ Oe L) 


The cells and cellular components of human blood are shown. 

Red blood cells deliver oxygen to the cells and remove carbon 

dioxide. White blood cells—including neutrophils, monocytes, 

lymphocytes, eosinophils, and basophils—are involved in the 

immune response. Platelets form clots that prevent blood loss 
after injury. 


Red Blood Cells 


Red blood cells, or erythrocytes (erythro- = “red”; -cyte = “cell’”), are 
specialized cells that circulate through the body delivering oxygen to cells; 
they are generated by division of stem cells in the bone marrow. In 
mammals, red blood cells are small biconcave cells that at maturity do not 
contain a nucleus or mitochondria and are only 7—8 pm in size. In birds and 
reptiles, erythrocytes have nuclie and mitochondria. 


The red coloring of human blood comes from the iron-containing protein 
hemoglobin, illustrated in [link]a. The principal job of these proteins is to 
carry oxygen, but they also transports carbon dioxide as well. Hemoglobin 
is packed into human red blood cells at a rate of about 250 million 


molecules of hemoglobin per cell. Each hemoglobin molecule binds four 
oxygen molecules so that each red blood cell carries one billion molecules 
of oxygen. There are approximately 25 trillion red blood cells in the five 
liters of blood in the human body, which could carry up to 25 sextillion (25 
x 10°!) molecules of oxygen in the body at any time. In mammals, the lack 
of organelles in erythrocytes leaves more room for the hemoglobin 
molecules, and the lack of mitochondria also prevents use of the oxygen for 
metabolic respiration. 


Not all organisms use hemoglobin as the method of oxygen transport. 
Invertebrates that utilize hemolymph rather than blood use different 
pigments to bind to the oxygen. These pigments use copper or iron to the 
oxygen. Invertebrates have a variety of other respiratory pigments. 
Hemocyanin, a blue-green, copper-containing protein, illustrated in [link]b 
is found in mollusks, crustaceans, and some of the arthropods. 
Chlorocruorin, a green-colored, iron-containing pigment is found in four 
families of polychaete tubeworms. Hemerythrin, a red, iron-containing 
protein is found in some polychaete worms and annelids and is illustrated in 
[link]c. Despite the name, hemerythrin does not contain a heme group and 
its oxygen-carrying capacity is poor compared to hemoglobin. 


Heme 


(a) Hemoglobin (b) Hemocyanin (c) Hemerythrin 


In most vertebrates, (a) hemoglobin delivers oxygen to the body 


and removes some carbon dioxide. Hemoglobin is composed of 
four protein subunits, two alpha chains and two beta chains, and a 
heme group that has iron associated with it. The iron reversibly 
associates with oxygen, and in so doing is oxidized from Fe2* to 
Fe**. In most mollusks and some arthropods, (b) hemocyanin 
delivers oxygen. Unlike hemoglobin, hemolymph is not carried in 
blood cells, but floats free in the hemolymph. Copper instead of 
iron binds the oxygen, giving the hemolymph a blue-green color. 
In annelids, such as the earthworm, and some other invertebrates, 
(c) hemerythrin carries oxygen. Like hemoglobin, hemerythrin is 
carried in blood cells and has iron associated with it, but despite 
its name, hemerythrin does not contain heme. 


The small size and large surface area of red blood cells allows for rapid 
diffusion of oxygen and carbon dioxide across the plasma membrane. In the 
lungs, carbon dioxide is released and oxygen is taken in by the blood. In the 
tissues, oxygen is released from the blood and carbon dioxide is bound for 
transport back to the lungs. 


White Blood Cells 


White blood cells, also called leukocytes (leuko = white), make up 
approximately one percent (by volume) of the cells in blood. The role of 
white blood cells is very different than that of red blood cells, as you have 
learned previously. They are primarily involved in the immune response to 
identify and target pathogens, such as invading bacteria, viruses, and other 
foreign organisms. White blood cells are formed continually; some only 
live for hours or days, but some live for years. 


The morphology of white blood cells differs significantly from red blood 
cells. They have nuclei and do not contain hemoglobin. The different types 
of white blood cells are identified by their microscopic appearance after 
histologic staining, and each has a different specialized function. The two 
main groups, both illustrated in [link] are the granulocytes, which include 


the neutrophils, eosinophils, and basophils, and the agranulocytes, which 
include the monocytes and lymphocytes. 


Granulocytes contain granules in their cytoplasm; the agranulocytes are so 
named because of the lack of granules in their cytoplasm. Some leukocytes 
become macrophages that either stay at the same site or move through the 
blood stream and gather at sites of infection or inflammation where they are 
attracted by chemical signals from foreign particles and damaged cells. 
Lymphocytes are the primary cells of the immune system and include B 
cells, T cells, and natural killer cells. B cells destroy bacteria and inactivate 
their toxins. They also produce antibodies. T cells attack viruses, fungi, 
some bacteria, transplanted cells, and cancer cells. T cells attack viruses by 
releasing toxins that kill the viruses. Natural killer cells attack a variety of 
infectious microbes and certain tumor cells. 


Platelets and Coagulation Factors 


Blood must clot to heal wounds and prevent excess blood loss. Small cell 
fragments called platelets (thrombocytes) are attracted to the wound site 
where they adhere by extending many projections and releasing their 
contents. These contents activate other platelets and also interact with other 
coagulation factors, which convert fibrinogen, a water-soluble protein 
present in blood serum into fibrin (a non-water soluble protein), causing the 
blood to clot. Many of the clotting factors require vitamin K to work, and 
vitamin K deficiency can lead to problems with blood clotting. Many 
platelets converge and stick together at the wound site forming a platelet 
plug (also called a fibrin clot), as illustrated in [link]b. The plug or clot lasts 
for a number of days and stops the loss of blood. Platelets are formed from 
the disintegration of larger cells called megakaryocytes, like that shown in 
[link]a. For each megakaryocyte, 2000-3000 platelets are formed with 
150,000 to 400,000 platelets present in each cubic millimeter of blood. 
Each platelet is disc shaped and 2—4 ym in diameter. They contain many 
small vesicles but do not contain a nucleus. 


Fibrin clot 


(b) 


(a) Platelets are formed from large cells called megakaryocytes. 
The megakaryocyte breaks up into thousands of fragments that 
become platelets. (b) Platelets are required for clotting of the 
blood. The platelets collect at a wound site in conjunction with 
other clotting factors, such as fibrinogen, to form a fibrin clot that 
prevents blood loss and allows the wound to heal. 


Plasma and Serum 


The liquid component of blood is called plasma, and it can separated from 
the blood cells by spinning or centrifuging the blood at high rotations (3000 
rpm or higher). The blood cells and platelets are separated by centrifugal 
forces to the bottom of a specimen tube. The upper liquid layer, the plasma, 
consists of 90 percent water along with various substances required for 
maintaining the body’s pH, osmotic load, and for protecting the body. The 
plasma also contains the coagulation factors and antibodies. 


The plasma component of blood without the coagulation factors is called 
the serum. Serum is similar to interstitial fluid in which the correct 


composition of key ions acting as electrolytes is essential for normal 
functioning of muscles and nerves. Other components in the serum include 
proteins that assist with maintaining pH and osmotic balance while giving 
viscosity to the blood. The serum also contains antibodies, specialized 
proteins that are important for defense against viruses and bacteria. Lipids, 
including cholesterol, are also transported in the serum, along with various 
other substances including nutrients, hormones, metabolic waste, plus 
external substances, such as, drugs, viruses, and bacteria. 


Note: 

Evolution Connection 

Blood Types Related to Proteins on the Surface of the Red Blood Cells 
Red blood cells are coated in antigens made of glycolipids and 
glycoproteins. The composition of these molecules is determined by 
genetics, which have evolved over time. In humans, the different surface 
antigens are grouped into 24 different blood groups with more than 100 
different antigens on each red blood cell. The two most well known blood 
groups are the ABO, shown in [link], and Rh systems. The surface antigens 
in the ABO blood group are glycolipids, called antigen A and antigen B. 
People with blood type A have antigen A, those with blood type B have 
antigen B, those with blood type AB have both antigens, and people with 
blood type O have neither antigen. Antibodies are found in the blood 
plasma can react with the A or B antigens; individuals with type A blood 
have antibodies to thye B blood cells. When type A and type B blood are 
combined, agglutination (clumping) of the blood occurs because of 
antibodies in the plasma that bind with the opposing antigen; this causes 
clots that coagulate in the kidney causing kidney failure and death. Type O 
blood has neither A or B antigens, and therefore, type O blood can be 
given to all blood types. Type O negative blood is the universal donor. 
Type AB positive blood is the universal acceptor because it has both A and 
B antigen. 


@ 


(0) (A) (B) 


Human red blood cells may have either type A or B 
glycoproteins on their surface, both glycoproteins 
combined (AB), or neither (O). The glycoproteins serve as 
antigens and can elicit an immune response in a person who 
receives a transfusion containing unfamiliar antigens. Type 
O blood, which has no A or B antigens, does not elicit an 
immune response when injected into a person of any blood 
type. Thus, O is considered the universal donor. Persons 
with type AB blood can accept blood from any blood type, 
and type AB is considered the universal acceptor. 


(AB) 


Mammalian Heart and Blood Vessels 


The heart is a complex muscle that pumps blood through the three divisions 
of the circulatory system: the coronary (vessels that serve the heart), 
pulmonary (heart and lungs), and systemic (systems of the body), as shown 
in [link]. Coronary circulation is intrinsic to the heart, and takes blood 
directly from the main artery (aorta) coming from the heart to provide 
oxygen for the hard-working heart muscle. For pulmonary and systemic 
circulation, the heart has to pump blood to the lungs or the rest of the body, 
respectively. In vertebrates, the lungs are relatively close to the heart in the 
thoracic cavity. The shorter distance to pump means that the heart muscle 
wall on the right side of the heart is not as thick as the left side which must 
have enough pressure to pump blood all the way to your big toe. 


Superior 
vena cava 


Right 
atrium 


Pulmonary 
artery 


Left atrium 
Pulmonary 


circuit 
Pulmonary 
vein 


Ses? Left ventricle 
Inferior | 


vena cava Systemic circuit 


Right 
ventricle 


The mammalian circulatory 
system is divided into three 
circuits: the systemic circuit, the 
pulmonary circuit, and the 
coronary circuit. Blood is pumped 
from veins of the systemic circuit 
into the right atrium of the heart, 
then into the right ventricle. Blood 
then enters the pulmonary circuit, 
and is oxygenated by the lungs. 
From the pulmonary circuit, blood 
re-enters the heart through the left 
atrium. From the left ventricle, 
blood re-enters the systemic 
circuit through the aorta and is 
distributed to the rest of the body. 
The coronary circuit, which 
provides blood to the heart, is not 
shown. 


Structure of the Heart 


The heart muscle is asymmetrical as a result of the distance blood must 
travel in the pulmonary and systemic circuits. Since the right side of the 
heart sends blood to the pulmonary circuit it is smaller than the left side 
which must send blood out to the whole body in the systemic circuit, as 
shown in [link]. In humans, the heart is about the size of a clenched fist; it 
is divided into four chambers: two atria and two ventricles. There is one 
atrium and one ventricle on the right side and one atrium and one ventricle 
on the left side. The atria are the chambers that receive blood from the 
circulation, and the ventricles are the chambers that pump blood into the 
circulation. The right atrium receives deoxygenated blood from the 
superior vena cava, which drains blood from the jugular vein that comes 
from the brain and from the veins that come from the arms, as well as from 
the inferior vena cava which drains blood from the veins that come from 
the lower organs and the legs. In addition, the right atrium receives blood 
from the coronary sinus which drains deoxygenated blood from the heart 
itself. This deoxygenated blood then passes to the right ventricle through 
the atrioventricular valve or the tricuspid valve. After it is filled, the right 
ventricle pumps the blood through the pulmonary arteries, by-passing the 
semilunar valve (or pulmonic valve) to the lungs for re-oxygenation. After 
blood passes through the pulmonary arteries, the right semilunar valves 
close preventing the blood from flowing backwards into the right ventricle. 
The left atrium then receives the oxygen-rich blood from the lungs via the 
pulmonary veins. This blood passes through the bicuspid valve or mitral 
valve (the atrioventricular valve on the left side of the heart) to the left 
ventricle where the blood is pumped out through aorta, the major artery of 
the body, taking oxygenated blood to the organs and muscles of the body. 
Once blood is pumped out of the left ventricle and into the aorta, the aortic 
semilunar valve (or aortic valve) closes preventing blood from flowing 
backward into the left ventricle. This pattern of pumping is referred to as 
double circulation and is found in all mammals. 


The heart has its own blood vessels that supply the heart muscle with blood. 
The coronary arteries branch from the aorta and surround the outer surface 
of the heart like a crown. They diverge into capillaries where the heart 
muscle is supplied with oxygen before converging again into the coronary 


veins to take the deoxygenated blood back to the right atrium where the 
blood will be re-oxygenated through the pulmonary circuit. The heart 
muscle will die without a steady supply of blood. Atherosclerosis is the 
blockage of an artery by the buildup of fatty plaques. Because of the size 
(narrow) of the coronary arteries and their function in serving the heart 
itself, atherosclerosis can be deadly in these arteries. The slowdown of 
blood flow and subsequent oxygen deprivation that results from 
atherosclerosis causes severe pain, known as angina, and complete blockage 
of the arteries will cause myocardial infarction: the death of cardiac muscle 
tissue, commonly known as a heart attack. 


Arteries, Veins, and Capillaries 


The blood from the heart is carried through the body by a complex network 
of blood vessels ([link]). Arteries take blood away from the heart. The 
main artery is the aorta that branches into major arteries that take blood to 
different limbs and organs. These major arteries include the carotid artery 
that takes blood to the brain, the brachial arteries that take blood to the 
arms, and the thoracic artery that takes blood to the thorax and then into the 
hepatic, renal, and gastric arteries for the liver, kidney, and stomach, 
respectively. The iliac artery takes blood to the lower limbs. The major 
arteries diverge into minor arteries, and then smaller vessels called 
arterioles, to reach more deeply into the muscles and organs of the body. 


Jugular 
veins 


Carotid 


Aorta artery 
Superior Pulmonary 
vena Cava arteries 
Inferior Pulmonary 
vena cava veins 
Brachial Heart 
ay Thoracic 
Basilic aorta 
ven Hepatic 


Gastric artery 


vein Gastric 
artery 


Renal 
artery 


lliac vein 


lliac artery 


The major human arteries and 
veins are shown. (credit: 
modification of work by 
Mariana Ruiz Villareal) 


Arterioles diverge into capillary beds. Capillary beds contain a large 
number (10 to 100) of capillaries that branch among the cells and tissues of 
the body. Capillaries are narrow-diameter tubes that can fit red blood cells 
through in single file and are the sites for the exchange of nutrients, waste, 
and oxygen with tissues at the cellular level. Fluid also crosses into the 
interstitial space from the capillaries. The capillaries converge again into 
venules that connect to minor veins that finally connect to major veins that 
take blood high in carbon dioxide back to the heart. Veins are blood vessels 
that bring blood back to the heart. The major veins drain blood from the 


same organs and limbs that the major arteries supply. Fluid is also brought 
back to the heart via the lymphatic system. 


Systems of Gas Exchange 


Introduction 

" The inspired and expired air may be sometimes very useful, by 
condensing and cooling the blood that passeth through the lungs; I hold that 
the depuration of the blood in that passage, is not only one of the ordinary, 
but one of the principal uses of respiration." Robert Boyle, in New 
Experiments ... Touching the Spring of Air, 1660 


The primary function of the respiratory system is to deliver oxygen to the 
cells of the body’s tissues and remove a waste product, carbon dioxide (the 
process which Boyle called "depuration"). The main structures of the 
human respiratory system are the nasal cavity, the trachea, and lungs, and 
these structures are what brings oxygen into the human body and removes 
carbon dioxide from the human body. As you learned previously, the 
circulatory system is responsible for moving oxygen from the lungs to the 
tissues and for moving carbon dioxide from the tissues and taking it to the 
lungs. At the cellular level the oxygen is needed to make ATP from the 
energy stored in glucose and other organic molecules; carbon dioxide is a 
waste product of harvesting that energy. In other words, the respiratory 
system gets the oxygen inside the body, the circulatory system moves the 
oxygen around the body getting it to the cells, the cells use the oxygen to 
produce energy and in the process produce carbon dioxide as a waste, the 
circulatory system removes the carbon dioxide from the cell and delivers it 
to the lungs, and the respiratory system removes the carbon dioxide from 
the body. In vertebrates, the respiratory and circulatory work very closely 
together in order to allow for gas exchange between the inside and outside 
of the organism. 


All aerobic organisms require oxygen to carry out their metabolic functions. 
Over evolutionary time, different organisms have devised different means 
of obtaining oxygen from the surrounding atmosphere. The environment in 
which the animal lives greatly determines how an animal respires. The 
complexity of the respiratory system is correlated with the size of the 
organism. As animal size increases, diffusion distances increase and the 
ratio of surface area to volume drops. In unicellular organisms, diffusion 
across the plasma membrane is sufficient for supplying oxygen to the cell 


({link]). Diffusion is a slow, passive transport process. Therefore, 
dependence on diffusion as a means of obtaining oxygen and removing 
carbon dioxide remains feasible only for small organisms or those with 
highly-flattened bodies, such as many flatworms (Platyhelminthes). Larger 
organisms had to evolve specialized respiratory tissues, such as gills, lungs, 
and respiratory passages accompanied by a complex circulatory systems, to 
transport oxygen throughout their entire body. 


The cell of the unicellular 


algae Ventricaria 
ventricosa is one of the 
largest known, reaching 
one to five centimeters in 
diameter. Like all single- 
celled organisms, V. 
ventricosa exchanges 
gases across the plasma 
membrane. 


Direct Diffusion 


For small multicellular organisms, diffusion across the outer membrane is 
sufficient to meet their oxygen needs. Gas exchange by direct diffusion 
across surface membranes is efficient for organisms less than 1 mm in 
diameter. In simple organisms, such as cnidarians and flatworms, every cell 


in the body is close to the external environment. Their cells are kept moist 
and gases diffuse quickly via direct diffusion. Flatworms are small, literally 
flat worms, which ‘breathe’ through diffusion across the outer surface 
({link]). The flat shape of these organisms increases the surface area for 
diffusion, ensuring that each cell within the body is close to the outer 
surface and has access to oxygen. If the flatworm had a cylindrical body, 
then the cells in the center would not be able to get oxygen. 


This flatworm’s process of 
respiration works by 
diffusion across the outer 
membrane. (credit: Stephen 
Childs) 


Skin and Gills 


Earthworms and amphibians use their skin (integument) as a respiratory 
organ. A dense network of capillaries lies just below the skin and facilitates 
gas exchange between the external environment and the circulatory system. 
The respiratory surface must be kept moist in order for the gases to dissolve 
and diffuse across plasma membranes. 


Organisms that live in water need to obtain oxygen from the water. Oxygen 
dissolves in water but at a lower concentration than in the atmosphere. The 


atmosphere has roughly 21 percent oxygen. In water, the oxygen 
concentration is much less than that. Fish and many other aquatic organisms 
have evolved gills to take up the dissolved oxygen from water ([link]). Gills 
are thin tissue filaments that are highly branched and folded. When water 
passes over the gills, the dissolved oxygen in water rapidly diffuses across 
the gills into the bloodstream. The circulatory system can then carry the 
oxygenated blood to the other parts of the body. In animals that contain 
coelomic fluid instead of blood, oxygen diffuses across the gill surfaces into 
the coelomic fluid. Gills are found in mollusks, annelids, and crustaceans. 


This common carp, like many 
other aquatic organisms, has gills 
that allow it to obtain oxygen from 
water. (credit: 
"Guitardude012"/Wikimedia 
Commons) 


The folded surfaces of the gills provide a large surface area to ensure that 
the fish gets sufficient oxygen. Diffusion is a process in which material 
travels from regions of high concentration to low concentration until 
equilibrium is reached. In this case, blood with a low concentration of 
oxygen molecules circulates through the gills. The concentration of oxygen 


molecules in water is higher than the concentration of oxygen molecules in 
gills. As a result, oxygen molecules diffuse from water (high concentration) 
to blood (low concentration), as shown in [link]. Similarly, carbon dioxide 
molecules in the blood diffuse from the blood (high concentration) to water 
(low concentration). 


Water flow 


Blood Lamella 
By vessels 
D 


Fy) 


4 


ri [> 
As Z 


Oxygen-rich 


"a 
Oxygen-poor 
blood 


Gill filaments 


As water flows over the gills, oxygen is transferred to blood via 
the veins. (credit "fish": modification of work by Duane Raver, 
NOAA) 


Tracheal Systems 


Insect respiration is independent of its circulatory system; therefore, the 
blood does not play a direct role in oxygen transport. Insects have a highly 
specialized type of respiratory system called the tracheal system, which 
consists of a network of small tubes that carries oxygen to the entire body. 
The tracheal system is the most direct and efficient respiratory system in 
active animals. 


Insect bodies have openings, called spiracles, along the thorax and 
abdomen. These openings connect to the tubular network, allowing oxygen 


to pass into the body ([link]) and regulating the diffusion of CO, and water 
vapor. Air enters and leaves the tracheal system through the spiracles. Some 
insects can ventilate the tracheal system with body movements. 


Tracheal system 


Insects perform respiration via a tracheal 
system. 


Mammalian Systems 


In mammals, pulmonary ventilation occurs via inhalation (breathing). 
During inhalation, air enters the human body through the nasal cavity 
located just inside the nose ({link]). As air passes through the nasal cavity, 
the air is warmed to body temperature and humidified. The respiratory tract 
is coated with mucus to seal the tissues from direct contact with air. Mucus 
is high in water. As air crosses these surfaces of the mucous membranes, it 
picks up water. These processes help equilibrate the air to the body 
conditions, reducing any damage that cold, dry air can cause. Particulate 
matter that is floating in the air is removed in the nasal passages via mucus 
and cilia. The processes of warming, humidifying, and removing particles 
are important protective mechanisms that prevent damage to the trachea and 
lungs. Thus, inhalation serves several purposes in addition to bringing 
oxygen into the respiratory system. 


Primary 
bronchus 


Nasal 
cavity 
Secondary 
bronchus 
Tertiary 
bronchus 


Pharynx 
Larynx 


Bronchiole Trachea 


Terminal 
bronchiole 


Pulmonary 
vein 


Alveolar sac 


Air enters the respiratory 
system through the nasal 
cavity and pharynx, and then 
passes through the trachea 
and into the bronchi, which 
bring air into the lungs. 
(credit: modification of work 
by NCI) 


From the nasal cavity, air passes through the pharynx (throat) and the 
larynx (voice box), as it makes its way to the trachea ([link]). The main 
function of the trachea is to funnel the inhaled air to the lungs and the 
exhaled air back out of the body. The human trachea is a cylinder about 10 
to 12 cm long and 2 cm in diameter that sits in front of the esophagus and 
extends from the larynx into the chest cavity where it divides into the two 
primary bronchi at the midthorax ([link]). The trachea is lined with mucus- 
producing goblet cells and ciliated epithelia. The cilia propel foreign 


particles trapped in the mucus toward the pharynx. The cartilage provides 
strength and support to the trachea to keep the passage open. The smooth 
muscle can contract, decreasing the trachea’s diameter, which causes 
expired air to rush upwards from the lungs at a great force. The forced 
exhalation helps expel mucus when we cough. Smooth muscle can contract 
or relax, depending on stimuli from the external environment or the body’s 
nervous system. 


Lungs: Bronchi and Alveoli 


The end of the trachea bifurcates (divides) to the right and left lungs. The 
lungs are not identical. The right lung is larger and contains three lobes, 
whereas the smaller left lung contains two lobes ({link]). The muscular 
diaphragm, which facilitates breathing, is inferior (below) to the lungs and 
marks the end of the thoracic cavity. 


Trachea 


Left lung 


Right lung Upper lobe 


Upper lobe 


; Lower lobe 
Middle lobe 


Lower lobe 
Diaphragm 


The trachea bifurcates into the 
right and left bronchi in the lungs. 
The right lung is made of three 
lobes and is larger. To 
accommodate the heart, the left 
lung is smaller and has only two 
lobes. 


In the lungs, air is diverted into smaller and smaller passages, or bronchi. 
Air enters the lungs through the two primary (main) bronchi (singular: 
bronchus). Each bronchus divides into secondary bronchi, then into tertiary 
bronchi, which in turn divide, creating smaller and smaller diameter 
bronchioles as they split and spread through the lung. 


The terminal bronchioles subdivide into microscopic branches called 
respiratory bronchioles. The respiratory bronchioles subdivide into several 
alveolar ducts. Numerous alveoli and alveolar sacs surround the alveolar 
ducts. The alveolar sacs resemble bunches of grapes tethered to the end of 
the bronchioles ({link]). Alveoli are made of thin-walled parenchymal cells, 
typically one-cell thick, that look like tiny bubbles within the sacs. Alveoli 
are in direct contact with capillaries (one-cell thick) of the circulatory 
system. Such intimate contact ensures that oxygen will diffuse from alveoli 
into the blood and be distributed to the cells of the body. In addition, the 
carbon dioxide that was produced by cells as a waste product will diffuse 
from the blood into alveoli to be exhaled. 


Alveolar sac Capillaries 


Alveolar duct 


Mucous gland 


Respiratory bronchiole Pulmonary vein 


Pulmonary artery Atrium Alveolus 


Terminal bronchioles are connected by respiratory bronchioles to 
alveolar ducts and alveolar sacs. Each alveolar sac contains 20 to 
30 spherical alveoli and has the appearance of a bunch of grapes. 
Air flows into the atrium of the alveolar sac, then circulates into 
alveoli where gas exchange occurs with the capillaries. Mucous 
glands secrete mucous into the airways, keeping them moist and 
flexible. (credit: modification of work by Mariana Ruiz Villareal) 


Transport of Gases in Blood 


Once the oxygen diffuses across the alveoli, it enters the bloodstream and is 
transported to the tissues where it is unloaded, and carbon dioxide diffuses 
out of the blood and into the alveoli to be expelled from the body. Although 
gas exchange is a continuous process, the oxygen and carbon dioxide are 
transported by different mechanisms. 


Transport of Oxygen in the Blood 


Although oxygen dissolves in blood, only a small amount of oxygen is 
transported this way. Only 1.5 percent of oxygen in the blood is dissolved 
directly into the blood itself. Most oxygen—98.5 percent—is bound to a 
protein called hemoglobin and carried to the tissues. 


Hemoglobin 


Hemoglobin, or Hb, is a protein molecule found in red blood cells 
(erythrocytes) made of four subunits: two alpha subunits and two beta 
subunits ({link]). Each subunit surrounds a central heme group that 
contains iron and binds one oxygen molecule, allowing each hemoglobin 
molecule to bind four oxygen molecules. Molecules with more oxygen 
bound to the heme groups are brighter red. As a result, oxygenated arterial 
blood where the Hb is carrying four oxygen molecules is bright red, while 
venous blood that is deoxygenated is darker red. 


Oxygen 


(a) Red blood cells (b) Hemoglobin 


The protein inside (a) red blood cells that carries oxygen to 
cells and carbon dioxide to the lungs is (b) hemoglobin. 
Hemoglobin is made up of four symmetrical subunits and 
four heme groups. Iron associated with the heme binds 
oxygen. It is the iron in hemoglobin that gives blood its red 
color. 


Transport of Carbon Dioxide in the Blood 


Carbon dioxide molecules are transported in the blood from body tissues to 
the lungs by one of three methods: dissolution directly into the blood, 
binding to hemoglobin, or carried as a bicarbonate ion. Several properties of 
carbon dioxide in the blood affect its transport. First, carbon dioxide is more 
soluble in blood than oxygen. About 5 to 7 percent of all carbon dioxide is 
dissolved in the plasma. Second, carbon dioxide can bind to plasma proteins 
or can enter red blood cells and bind to hemoglobin. This form transports 
about 10 percent of the carbon dioxide. When carbon dioxide binds to 
hemoglobin, a molecule called carbaminohemoglobin is formed. Binding of 
carbon dioxide to hemoglobin is reversible. Therefore, when it reaches the 
lungs, the carbon dioxide can freely dissociate from the hemoglobin and be 
expelled from the body. 


Third, the majority of carbon dioxide molecules (85 percent) are carried as 
part of the bicarbonate buffer system. In this system, carbon dioxide 
diffuses into the red blood cells. Carbonic anhydrase (CA) within the red 
blood cells quickly converts the carbon dioxide into carbonic acid (H»COs3). 
Carbonic acid is an unstable intermediate molecule that immediately 
dissociates into bicarbonate ions (HCO, ) and hydrogen (H") ions. Since 
carbon dioxide is quickly converted into bicarbonate ions, this reaction 
allows for the continued uptake of carbon dioxide into the blood down its 
concentration gradient. It also results in the production of H” ions. If too 
much H” is produced, it can alter blood pH. However, hemoglobin binds to 
the free H* ions and thus limits shifts in pH. The newly synthesized 
bicarbonate ion is transported out of the red blood cell into the plasma of 
the blood in exchange for a chloride ion (Cl); this is called the chloride 
shift. When the blood reaches the lungs, the bicarbonate ion is transported 
back into the red blood cell in exchange for the chloride ion. The H” ion 
dissociates from the hemoglobin and binds to the bicarbonate ion. This 
produces the carbonic acid intermediate, which is converted back into 


carbon dioxide through the enzymatic action of CA. The carbon dioxide 
produced is expelled through the lungs during exhalation. 
Equation: 


H2CO3 HCO; + H* 


H 
CO.+H20 © (carbonic acid) (bicarbonate) 


The benefit of the bicarbonate buffer system is that carbon dioxide is 
“soaked up” into the blood with little change to the pH of the system. This 
is important because it takes only a small change in the overall pH of the 
body for severe injury or death to result. The presence of this bicarbonate 
buffer system also allows for people to travel and live at high altitudes: 
When the partial pressure of oxygen and carbon dioxide change at high 
altitudes, the bicarbonate buffer system adjusts to regulate carbon dioxide 
while maintaining the correct pH in the body. 


Nervous System 


Introduction 

"We can trace the development of a nervous system, and correlate with it 
the parallel phenomena of sensation and thought. We see with undoubting 
certainty that they go hand-in-hand. But we try to soar in a vacuum the 
moment we seek to comprehend the connexion between them... Man the 
object is separated by an impassable gulf from man the subject." John 
Tyndall, British physicist, in Fragments of Science for Unscientific People: 
A Series of Detached Essays, Lectures and Reviews, 1892 


The distinction between the brain and the mind, as described by Tyndall, is 
but one of many questions that have fascinated scientists regarding the 
human nervous system. Several Nobel Prizes have been awarded to 
scientists who have helped elucidate the workings of nerves and nervous 
systems, usually with the aid of studies in non-human organisms. 


While you’re reading this, your nervous system is performing several 
functions simultaneously. The visual system is processing what is seen on 
the page; the motor system controls the turn of the pages (or click of the 
mouse); the prefrontal cortex maintains attention. Even fundamental 
functions, like breathing and regulation of body temperature, are controlled 
by the nervous system. A nervous system is an organism’s control center: it 
processes sensory information from outside (and inside) the body and 
controls all behaviors—from eating to sleeping to studying to finding a 
mate. 


Diversity of Nervous Systems 


Nervous systems throughout the animal kingdom vary in structure and 
complexity, as illustrated by the variety of animals shown in [link]. Some 
organisms, like sea sponges, lack a true nervous system. Others, like 
jellyfish, lack a true brain and instead have a system of separate but 
connected nerve cells (neurons) called a “nerve net.” Echinoderms such as 
sea Stars have nerve cells that are bundled into fibers called nerves. 
Flatworms of the phylum Platyhelminthes have both a central nervous 
system (CNS), made up of a small “brain” and two nerve cords, and a 


peripheral nervous system (PNS) containing a system of nerves that extend 
throughout the body. The insect nervous system is more complex but also 
fairly decentralized. It contains a brain, ventral nerve cord, and ganglia 
(clusters of connected neurons). These ganglia can control movements and 
behaviors without input from the brain. Octopi may have the most 
complicated of invertebrate nervous systems—they have neurons that are 


organized in specialized lobes and eyes that are structurally similar to 
vertebrate species. 


Eyespot 


\ 


L 


Central 
ganglia 
(brain) 


Nerve ring 


‘4. Transverse 


Radial nerve 


nerves 
(a) Cnidarian (b) Echinoderm (c) Planarian 
(hydra) ‘sea Star} (flatworm) 


Central nervous system 


Central ganglia 
(brain) 


Ganglia 


Peripheral 
ake nervous 


19/7 system 
Segmental ganglia Nerve 


(d) Arthropod (e) Mollusk (f) Vertebrate 
(bee) (octopus) (human) 


Nervous systems vary in structure and 
complexity. In (a) cnidarians, nerve cells 
form a decentralized nerve net. In (b) 
echinoderms, nerve cells are bundled into 
fibers called nerves. In animals exhibiting 
bilateral symmetry such as (c) planarians, 
neurons cluster into an anterior brain that 
processes information. In addition to a brain, 
(d) arthropods have clusters of nerve cell 


bodies, called peripheral ganglia, located 
along the ventral nerve cord. Mollusks such 
as squid and (e) octopi, which must hunt to 
survive, have complex brains containing 
millions of neurons. In (f) vertebrates, the 
brain and spinal cord comprise the central 
nervous system, while neurons extending 
into the rest of the body comprise the 
peripheral nervous system. (credit e: 
modification of work by Michael Vecchione, 
Clyde F.E. Roper, and Michael J. Sweeney, 
NOAA; credit f: modification of work by 
NIH) 


Compared to invertebrates, vertebrate nervous systems are more complex, 
centralized, and specialized. While there is great diversity among different 
vertebrate nervous systems, they all share a basic structure: a CNS that 
contains a brain and spinal cord and a PNS made up of peripheral sensory 
and motor nerves. One interesting difference between the nervous systems 
of invertebrates and vertebrates is that the nerve cords of many 
invertebrates are located ventrally whereas the vertebrate spinal cords are 
located dorsally. There is debate among evolutionary biologists as to 
whether these different nervous system plans evolved separately or whether 
the invertebrate body plan arrangement somehow “flipped” during the 
evolution of vertebrates. 


Neurons and Glial Cells 


The nervous system is made up of neurons, specialized cells that can 
receive and transmit chemical or electrical signals, and glia, cells that 
provide support functions for the neurons by playing an information 
processing role that is complementary to neurons. A neuron can be 
compared to an electrical wire—it transmits a signal from one place to 
another. Glia can be compared to the workers at the electric company who 
make sure wires go to the right places, maintain the wires, and take down 


wires that are broken. This analogy might be oversimplified, however; 
recent evidence suggests that glial cells also usurp some of the signaling 
functions of neurons. 


The nervous system of the common laboratory fly, Drosophila 
melanogaster, contains around 100,000 neurons, the same number as a 
lobster. This number compares to 75 million in the mouse and 300 million 
in the octopus. A human brain contains around 86 billion neurons. Despite 
these very different numbers, the nervous systems of these animals control 
many of the same behaviors—from basic reflexes to more complicated 
behaviors like finding food and courting mates. The ability of neurons to 
communicate with each other as well as with other types of cells underlies 
all of these behaviors. 


There is great diversity in the types of neurons and glia that are present in 
different parts of the nervous system. There are three major functional types 
of neurons (and many different morphological types), and they share 
several important cellular components. But neurons are also highly 
specialized—different types of neurons have different sizes and shapes that 
relate to their functional roles. There are also several types of glial cells 
(astroglia, oligodendrocytes, Schwann cells, etc.) each with different 
functions. 


Neurons 


Parts of a Neuron 


Like other cells, each neuron has a cell body (or soma) that contains a 
nucleus, smooth and rough endoplasmic reticulum, Golgi apparatus, 
mitochondria, and other cellular components. Neurons also contain unique 
structures, illustrated in [link] for receiving and sending the electrical 
signals that make neuronal communication possible. Dendrites are tree-like 
structures that extend away from the cell body to receive messages from 
other neurons at specialized junctions called synapses. Although some 


neurons do not have any dendrites, some types of neurons have multiple 
dendrites. 


Once a signal is received by the dendrite, it then travels to the cell body. 
The cell body contains a specialized structure, the axon hillock, that 
integrates signals from multiple synapses and serves as a junction between 
the cell body and an axon. An axon is a tube-like structure that propagates 
the integrated signal to specialized endings called axon terminals. These 
terminals in turn synapse on other neurons, muscle, or target organs. 
Chemicals (known as neurotransmitters) released at axon terminals allow 
signals to be communicated to these other cells. Neurons usually have one 
or two axons, but some neurons, like amacrine cells in the retina, do not 
contain any axons. Some axons are covered with myelin (a product of the 
glial cells), which acts as an insulator and greatly increases the speed of 
conduction. Along the axon there are periodic gaps in the myelin sheath. 
These gaps are called nodes of Ranvier and are sites where the signal is 
“recharged” as it travels along the axon. 


It is important to note that a single neuron does not act alone—neuronal 
communication depends on the connections that neurons make with one 
another (as well as with other cells, like muscle cells). Dendrites from a 
single neuron may receive synaptic contact from many other neurons. For 
example, dendrites from a Purkinje cell in the cerebellum are thought to 
receive contact from as many as 200,000 other neurons. 


Note: 


Cell body (soma) 


A 


4s 4 2 ye 
XH 


Axon Oligodendrocyte 


Cell membrane 


Dendrite e—? 
Node of Ranvier 


Myelin sheath 


Synapse 


Neurons contain organelles common to many other cells, 
such as a nucleus and mitochondria. They also have more 
specialized structures, including dendrites and axons. 


Types of Neurons 


There are different types of neurons, and the functional role of a given 
neuron is intimately dependent on its structure. Although there are only 
three functional types of neurons [link], an amazing diversity of neuron 
shapes and sizes can found in different parts of the nervous system (and 
across species). 

Neuron Types 


receptor endings 


A. Sensory 


dendrites ~ 

oN 
Us 
(S— 


y 


axon terminals 
axon 


a. B: Interneuron 
pl 


dendrites 


a 
> — 
=> 


C.Motor | es 
neuron 


The three general classes of neurons; all have an input zone (recpetor 
endings, dendrites and/or the cell body), an axon, a cell body, and an 
output zone (axon terminals). A. Sensory neurons have receptor 
endings at one end that are sensitive to various stimuli (e.g. heat, 
pressure, light, etc.), a relatively long axon, and axon terminals that 
form synapses with dendrites at the other end. B. interneurons receive 
signals from sensory neurons via their dendrites at one end, have a 
relatively short axon, and pass signals to another neuron via axon 
terminals at the other end. C. Motor neurons receive signals via 
dendrites at one end, have a long axon, and transmit signals to muscles 
or glands at the other end. (Image by Eva Horne) 


While there are many defined neuron cell shapes, neurons are broadly 
divided into three basic types: sensory, interneuron, and motor neuron. In 
general, sensory neurons detect information, either from the external 
environment or from internal sources. Examples of sensory neurons include 
the pain receptors in your skin and the photoreceptors in your retina. When 
activated by the signal to which they are attuned, they send information (via 
an action potential) to an interneuron. Interneurons both receive signals 
from other neurons and transmit signals to other neurons. The majority of 
the cells in your brain and spinal cord are interneurons, communicating 


only with other neurons. Interneurons can also send a signal to motor 
neurons, which control muscles and endocrine glands. 


Glia 


While glia are often thought of as the supporting cast of the nervous system, 
the number of glial cells in the human brain actually outnumbers the 
number of neurons by a factor of ten. Neurons would be unable to function 
without the vital roles that are fulfilled by these glial cells. Glia guide 
developing neurons to their destinations, buffer ions and chemicals that 
would otherwise harm neurons, contribute to the formation of cerebrospinal 
fluid, and provide myelin sheaths around axons. Scientists have recently 
discovered that they also play a role in responding to nerve activity and 
modulating communication between nerve cells. When glia do not function 
properly, the result can be disastrous—most brain tumors are caused by 
mutations in glia. 


How Neurons Communicate 


All functions performed by the nervous system—from a simple motor 
reflex to more advanced functions like making a memory or a decision— 
require neurons to communicate with one another. While humans use words 
and body language to communicate, neurons use electrical and chemical 
signals. Just like a person in a committee, one neuron usually receives and 
synthesizes messages from multiple other neurons before “making the 
decision” to send the message on to other neurons. 


Nerve Impulse Transmission within a Neuron 


For the nervous system to function, neurons must be able to send and 
receive signals. These signals are possible because each neuron has a 
charged cellular membrane (a voltage difference between the inside and the 
outside), and the charge of this membrane can change in response to 
neurotransmitter molecules released from other neurons and environmental 


stimuli. To understand how neurons communicate, one must first 
understand the basis of the baseline or ‘resting’ membrane charge. 


Neuronal Charged Membranes 


The lipid bilayer membrane that surrounds a neuron is impermeable to 
charged molecules or ions. To enter or exit the neuron, ions must pass 
through special proteins called ion channels that span the membrane. Ion 
channels have different configurations: open, closed, and inactive, as 
illustrated in [link]. Some ion channels need to be activated in order to open 
and allow ions to pass into or out of the cell. These ion channels are 
sensitive to the environment and can change their shape accordingly. Ion 
channels that change their structure in response to voltage changes are 
called voltage-gated ion channels. Voltage-gated ion channels regulate the 
relative concentrations of different ions inside and outside the cell. The 
difference in total charge between the inside and outside of the cell is called 
the membrane potential. 


Voltage-gated Na* Channels 


Outside cell 


CEASE AE 25 AE 25 2 4 


| 


OQOOOC™ 


Cytoplasm 
Closed At the resting potential, the Open In response to a nerve impulse, Inactivated For a brief period following 
channel is closed. the gate opens and Na* enters the cell. activation, the channel does not open 


in response to a new signal. 


Voltage-gated ion channels open in response to changes in 
membrane voltage. After activation, they become inactivated 
for a brief period and will no longer open in response to a 
signal. 


Resting Membrane Potential 


A neuron at rest is negatively charged: the inside of a cell is approximately 
70 millivolts more negative than the outside (—70 mV, note that this number 
varies by neuron type and by species). This voltage is called the resting 
membrane potential; it is generated by differences in the concentrations of 
ions inside and outside the cell. If the membrane were equally permeable to 
all ions, each type of ion would flow across the membrane and the system 
would reach equilibrium. Because ions cannot freely cross the membrane, 
and because enzymes can pump ions into or out of a cell, there are different 
concentrations of several ions inside and outside the cell, as shown in [link]. 
The difference in the number of positively charged potassium ions (K*) 
inside and outside the cell dominates the resting membrane potential 
({link]). When the membrane is at rest, K* ions accumulate inside the cell. 
The negative resting membrane potential is created and maintained by 
increasing the concentration of cations outside the cell (in the extracellular 
fluid) relative to inside the cell (in the cytoplasm); with more positive ions 
outside than inside, the inside of the cell is negatively charged (-70mV) 
compared to the extracellular space. The negative charge within the cell is 
created by the plasma membrane being more permeable to potassium ion 
movement than sodium ion movement. In neurons, potassium ions are 
maintained at high concentrations within the cell while sodium ions are 
maintained at high concentrations outside of the cell. The cell possesses 
potassium and sodium leakage channels that allow the two cations to 
diffuse down their concentration gradient. However, the neurons have far 
more potassium leakage channels than sodium leakage channels. Therefore, 
potassium diffuses out of the cell at a much faster rate than sodium leaks in. 
Because more cations are leaving the cell than are entering, this causes the 
interior of the cell to be negatively charged relative to the outside of the 
cell. The actions of the sodium potassium pump help to maintain the resting 
potential, once established. Recall that sodium potassium pumps brings two 
K" ions into the cell while removing three Na* ions per ATP consumed. As 
more cations are expelled from the cell than taken in, the inside of the cell 
remains negatively charged relative to the extracellular fluid. It should be 


noted that chloride ions (CI-) tend to accumulate outside of the cell because 
they are repelled by negatively-charged proteins within the cytoplasm. 


Ion Concentration Inside and Outside Neurons 


Extracellular Intracellular 
concentration concentration Ratio 
Ion (mM) (mM) outside/inside 
Na‘ 145 12 12 
K+ 4 155 0.026 
Cl" 120 4 30 
Organic 
anions — 100 
(A-) 


The resting membrane potential is a result of different concentrations inside 
and outside the cell. 


(a) Resting potential 


Extracellular fluid (@) Na’) 
() (a) ©) (i) Nat channel 


yes 
é LOOO0OX-"L OOCT z NeeooaaoN\ faNooue 
i) | 
! | 
) ; } ) 
Mt : | ; 
©00000000008 100000000 00000000— 000000006 00000006 
Qs y\ (3) 


@~ © @ © = © 
Nat /K* transporter 


At the resting potential, all voltage-gated Na* channels and most voltage-gated K* channels are closed. The Na*/K* transporter 
pumps K’* ions into the cell and Na* ions out. 


(b) Depolarization 


Na’ channel 


«) Nat /K* transporter (x) (ve) («) «) 
In response to a depolarization, some Na* channels open, allowing Na* ions to enter the cell. The membrane starts to depolarize 
(the charge across the membrane lessens). If the threshold of excitation is reached, all the Na* channels open. 


(c) Hyperpolarization 


K* channel 
COOCOCCOCCCOO MM M00 CCCCCE/AM M0CCCCCCe' MD MF \e0e0ee8 


OOOOOOOOOOOOW OOOO OOOO OOOOH OHO — 


() ©... /K* transporter 
At the peak action potential, Na* channels close while K* channels open. K* leaves the cell, and the membrane eventually 
becomes hyperpolarized. 


The (a) resting membrane potential is a result of 
different concentrations of Na* and K” ions inside 
and outside the cell. A nerve impulse causes Na* 
to rapidly enter the cell, resulting in (b) 
depolarization. At the peak action potential, K* 
channels open and the cell becomes (c) 
hyperpolarized. 


Action Potential 


A neuron can receive input from other neurons and, if this input is strong 
enough, send the signal to downstream neurons. Transmission of a signal 
between neurons is generally dependent on chemicals we call 
neurotransmitters, which move between nerve cells and their targets. 
Transmission of a signal within a neuron (from dendrite to axon terminal) is 
initiated by a brief reversal of the resting membrane potential called an 
action potential. When neurotransmitter molecules bind to receptors 
located on a neuron’s dendrites, ion channels open. At excitatory synapses, 
this opening allows positive ions to enter the neuron and results in 
depolarization of the membrane—a decrease in the difference in voltage 
between the inside and outside of the neuron. A stimulus from a sensory 
cell or another neuron depolarizes the target neuron to its threshold 
potential (-55 mV). Na* channels in the axon hillock open, allowing 
positive ions to enter the cell ([link] and [link]). Once the sodium channels 
open, the neuron completely depolarizes to a membrane potential of about 
+40 mV. Action potentials are considered an "all-or nothing" event, in that, 
once the threshold potential is reached, the neuron always completely 
depolarizes. Once depolarization is complete, the cell must now "reset" its 
membrane voltage back to the resting potential. To accomplish this, the Na* 
channels close and cannot be opened. This begins the neuron's refractory 
period, in which it cannot produce another action potential because its 
sodium channels will not open. At the same time, voltage-gated K* 
channels open, allowing K* to leave the cell. As K* ions leave the cell, the 
membrane potential once again becomes negative. The diffusion of K* out 
of the cell actually hyperpolarizes the cell, in that the membrane potential 
becomes more negative than the cell's normal resting potential. At this 
point, the sodium channels will return to their resting state, meaning they 
are ready to open again if the membrane potential again exceeds the 
threshold potential. 


Note: 


Membrane potential (mV) 


+30 


Repolarization 


Threshold of 
excitation 


Hyperpolarization 


Time 


The formation of an action 
potential can be divided into 
five steps: (1) A stimulus from a 
sensory cell or another neuron 
causes the target cell to 
depolarize toward the threshold 
potential. (2) If the threshold of 
excitation is reached, all Na* 
channels open and the 
membrane depolarizes. (3) At 
the peak action potential, K* 
channels open and K* begins to 
leave the cell. At the same time, 
Na* channels close. (4) The 
membrane becomes 
hyperpolarized as K* ions 
continue to leave the cell. The 
hyperpolarized membrane is in 
a refractory period and cannot 
fire. (5) The K* channels close 
and the Na*/K* transporter 
restores the resting potential. 


Peak action potential 


ee 


Direction of travel of action potential 


a. In response to a signal, the 
soma end of the axon becomes 
depolarized. 


b. The depolarization spreads down 
the axon. Meanwhile, the first part of 
the membrane repolarizes. Because 
Na* channels are inactivated and 
additional K* channels have opened, 
the membrane cannot depolarize again. 


c. The action potential continues to 
travel down the axon. 


The action potential is conducted down the axon as the axon 
membrane depolarizes, then repolarizes. 


Synaptic Transmission 


The synapse or “gap” is the place where information is transmitted from 
one neuron to another. Synapses usually form between axon terminals and 
dendritic spines, but this is not universally true. There are also axon-to- 
axon, dendrite-to-dendrite, and axon-to-cell body synapses. The neuron 
transmitting the signal is called the presynaptic neuron, and the neuron 
receiving the signal is called the postsynaptic neuron. Note that these 
designations are relative to a particular synapse—most neurons are both 
presynaptic and postsynaptic. There are two types of synapses: chemical 
and electrical. 


Chemical Synapse 


When an action potential reaches the axon terminal it depolarizes the 
membrane and opens voltage-gated Na* channels. Na* ions enter the cell, 
further depolarizing the presynaptic membrane. This depolarization causes 
voltage-gated Ca** channels to open. Calcium ions entering the cell initiate 
a signaling cascade that causes small membrane-bound vesicles, called 
synaptic vesicles, containing neurotransmitter molecules to fuse with the 
presynaptic membrane. Synaptic vesicles are shown in [link], which is an 
image from a scanning electron microscope. 


This pseudocolored image taken 
with a scanning electron 
microscope shows an axon 
terminal that was broken open to 
reveal synaptic vesicles (blue and 
orange) inside the neuron. (credit: 
modification of work by Tina 
Carvalho, NIH-NIGMS; scale-bar 
data from Matt Russell) 


Fusion of a vesicle with the presynaptic neuronal plasma membrane causes 
neurotransmitter to be released into the synaptic cleft, the extracellular 
space between the presynaptic and postsynaptic cells, as illustrated in [link]. 
The neurotransmitter diffuses across the synaptic cleft and binds to receptor 
proteins on the postsynaptic cell's plasma membrane. 


pS Presynaptic 
neuron 


©@ Action potential 
arrives at axon 
terminal. 


Axon terminal 


Ca?* entry causes 
neurotransmitter-containing 
synaptic vesicles to release 
their contents by exocytosis. 


Synaptic 
vesicles 


Synaptic cleft @ Voltage-gated Ca2* 
channels open and 
Ca?* enters the 


axon terminal. 


Neurotransmitter diffuses across 
the synaptic cleft and binds to 
ligand-gated ion channels on the 
postsynaptic membrane. 


Localized membrane 
potential 


lon movement 
if 


(2 a 


SHH SECEHOSESOALOE 


Binding of neurotransmitter opens ligand-gated © Reuptake by the presynapic neuron, enzymatic degradation, 
ion channels, resulting in graded potentials. and diffusion reduce neurotransmitter levels, terminating the 
signal. 


Communication at chemical synapses requires release of 


neurotransmitters. When the presynaptic membrane is 
depolarized, voltage-gated Ca** channels open and allow 
Ca?* to enter the cell. The calcium entry causes synaptic 
vesicles to fuse with the membrane and release 
neurotransmitter molecules into the synaptic cleft. The 
neurotransmitter diffuses across the synaptic cleft and 
binds to ligand-gated ion channels in the postsynaptic 
membrane, resulting in a localized depolarization or 
hyperpolarization of the postsynaptic neuron. 


The binding of a specific neurotransmitter causes particular ion channels on 
the postsynaptic membrane to open. Unlike the sodium channels which 
respond to a change in the membrane voltage (i.e., voltage-gated channels), 
these ion channels are classified as ligand-gated, since they open the gates 
in response to binding of the ligand (neurotransmitter). Neurotransmitters 
can either have excitatory or inhibitory effects on the postsynaptic 
membrane, as detailed in [link]. For example, when acetylcholine is 
released at the synapse between a nerve and muscle (called the 
neuromuscular junction) by a presynaptic neuron, it causes postsynaptic 
Na* channels to open. Na’ enters the postsynaptic cell and causes the 
postsynaptic membrane to depolarize. 


Once neurotransmission has occurred, the neurotransmitter must be 
removed from the synaptic cleft so the postsynaptic membrane can “reset” 
and be ready to receive another signal. This can be accomplished in three 
ways: the neurotransmitter can diffuse away from the synaptic cleft, it can 
be degraded by enzymes in the synaptic cleft, or it can be recycled 
(sometimes called re-uptake) by the presynaptic neuron. Several drugs act 
at this step of neurotransmission. For example, cocaine acts to inhibit re- 
uptake of neurotransmitters, which acts to prolong the excitatory stimulus 
initiated by those neurotransmitters. Many of the well-known antidepressant 
drugs work in the same way. 


Neurotransmitter Function and Location 


Neurotransmitter Example Location 
CNS 

Acetylcholine — and/or 
PNS 
CNS 


Dopamine, serotonin, 


Biogenic amine nGrenasehiine and/or 
pinep PNS 
Read Glycine, glutamate, aspartate, CNS 
gamma aminobutyric acid 
CNS 
Neuropeptide Substance P, endorphins and/or 
PNS 


Electrical Synapses 


While electrical synapses are fewer in number than chemical synapses, they 
are found in all nervous systems and play important and unique roles. The 
mode of neurotransmission in electrical synapses is quite different from that 
in chemical synapses. In an electrical synapse, the presynaptic and 
postsynaptic membranes are very close together and are actually physically 
connected by channel proteins forming gap junctions. Gap junctions allow 
current to pass directly from one cell to the next. In addition to the ions that 
carry this current, other molecules (e.g. ATP, or signaling ions like Ca**), 
can diffuse through the large gap junction pores. 


There are key differences between chemical and electrical synapses. 
Because chemical synapses depend on the release of neurotransmitter 
molecules from synaptic vesicles to pass on their signal, there is an 
approximately one millisecond delay between when the axon potential 


reaches the presynaptic terminal and when the neurotransmitter leads to 
opening of postsynaptic ion channels. Additionally, this signaling is 
unidirectional. Signaling in electrical synapses, in contrast, is virtually 
instantaneous (which is important for synapses involved in key reflexes), 
and some electrical synapses are bidirectional. Electrical synapses are also 
more reliable as they are less likely to be blocked, and they are important 
for synchronizing the electrical activity of a group of neurons. For example, 
electrical synapses in the thalamus are thought to regulate slow-wave sleep, 
and disruption of these synapses can cause seizures. 


Central Nervous System 


The central nervous system (CNS) is made up of the brain, a part of which 
is shown in [link] and spinal cord and is covered with three layers of 
protective coverings called meninges (from the Greek word for membrane). 
The outermost layer is the dura mater (Latin for “hard mother”). As the 
Latin suggests, the primary function for this thick layer is to protect the 
brain and spinal cord. The dura mater also contains vein-like structures that 
carry blood from the brain back to the heart. The middle layer is the web- 
like arachnoid mater. The last layer is the pia mater (Latin for “soft 
mother”), which directly contacts and covers the brain and spinal cord like 
plastic wrap. The space between the arachnoid and pia maters is filled with 
cerebrospinal fluid (CSF). CSF is produced by a tissue called choroid 
plexus in fluid-filled compartments in the CNS called ventricles. The brain 
floats in CSF, which acts as a cushion and shock absorber and makes the 
brain neutrally buoyant. CSF also functions to circulate chemical 
substances throughout the brain and into the spinal cord. 


The entire brain contains only about 8.5 tablespoons of CSF, but CSF is 
constantly produced in the ventricles. This creates a problem when a 
ventricle is blocked—the CSF builds up and creates swelling and the brain 
is pushed against the skull. This swelling condition is called hydrocephalus 
(“water head”) and can cause seizures, cognitive problems, and even death 
if a shunt is not inserted to remove the fluid and pressure. 


Skin Veins 


Dura mater Arachnoid 


mater 


Pia mater Cerebral 


cortex 


The cerebral cortex is covered by 
three layers of meninges: the dura, 
arachnoid, and pia maters. (credit: 
modification of work by Gray’s 
Anatomy) 


Brain 


The brain is the part of the central nervous system that is contained in the 
cranial cavity of the skull. It includes the cerebral cortex, limbic system, 
basal ganglia, thalamus, hypothalamus, and cerebellum. There are three 
different ways that a brain can be sectioned in order to view internal 
structures: a Sagittal section cuts the brain left to right, as shown in [link]b, 
a coronal section cuts the brain front to back, as shown in [link]a, and a 
horizontal section cuts the brain top to bottom. 


Cerebral Cortex 


The outermost part of the brain is a thick piece of nervous system tissue 
called the cerebral cortex, which is folded into hills called gyri (singular: 
gyrus) and valleys called sulci (singular: sulcus). The cortex is made up of 
two hemispheres—right and left—which are separated by a large sulcus. A 
thick fiber bundle called the corpus callosum (Latin: “tough body”) 
connects the two hemispheres and allows information to be passed from one 
side to the other. Although there are some brain functions that are localized 
more to one hemisphere than the other, the functions of the two 
hemispheres are largely redundant. In fact, sometimes (very rarely) an 
entire hemisphere is removed to treat severe epilepsy. While patients do 
suffer some deficits following the surgery, they can have surprisingly few 
problems, especially when the surgery is performed on children who have 
very immature nervous systems. 


Corpus callosum 


Basal { > 
ganglia " 
Gyri \ 


Right 
hemisphere 
of the 
cerebral 
cortex 


Thalamus 


Amygdala Cerebellum 


Cerebellum Brainstem 


(a) Coronal section (b) Sagittal section 


Brainstem 


These illustrations show the (a) coronal and (b) sagittal 
sections of the human brain. 


Each cortical hemisphere contains regions called lobes that are involved in 
different functions. Scientists use various techniques to determine what 
brain areas are involved in different functions: they examine patients who 
have had injuries or diseases that affect specific areas and see how those 
areas are related to functional deficits. They also conduct animal studies 
where they stimulate brain areas and see if there are any behavioral 
changes. They use a technique called transmagnetic stimulation (TMS) to 


temporarily deactivate specific parts of the cortex using strong magnets 
placed outside the head; and they use functional magnetic resonance 
imaging (fMRI) to look at changes in oxygenated blood flow in particular 
brain regions that correlate with specific behavioral tasks. These techniques, 
and others, have given great insight into the functions of different brain 
regions but have also showed that any given brain area can be involved in 
more than one behavior or process, and any given behavior or process 
generally involves neurons in multiple brain areas. That being said, each 
hemisphere of the mammalian cerebral cortex can be broken down into four 
functionally and spatially defined lobes: frontal, parietal, temporal, and 
occipital. [link] illustrates these four lobes of the human cerebral cortex. 


Motor cortex 


Somatosensory 
cortex 

Frontal lobe 
Parietal lobe 


Olfactory bulb 
Temporal lobe 


Cerebellum 


Spinal cord 


The human cerebral cortex 
includes the frontal, parietal, 
temporal, and occipital lobes. 


The frontal lobe is located at the front of the brain, over the eyes. This lobe 
contains the olfactory bulb, which processes odors. The frontal lobe also 
contains the motor cortex, which is important for planning and 
implementing movement. Areas within the motor cortex map to different 
muscle groups, and there is some organization to this map, as shown in 
[link]. For example, the neurons that control movement of the fingers are 


next to the neurons that control movement of the hand. Neurons in the 
frontal lobe also control cognitive functions like maintaining attention, 
speech, and decision-making. Studies of humans who have damaged their 
frontal lobes show that parts of this area are involved in personality, 
socialization, and assessing risk. 


Wrists . 
Elbows Fingers 


Shoulders 


Thumbs 


Eyebrows 
and eyelids 


Eyeballs 


Face 


Cerebral 


cortex ma 


Jaw 


Tongue 
Motor cortex 
(right hemisphere) 
Salivation 


Chewing 


Swallowing 


Different parts of the motor 
cortex control different muscle 
groups. Muscle groups that are 

neighbors in the body are 
generally controlled by 
neighboring regions of the 
motor cortex as well. For 
example, the neurons that 
control finger movement are 
near the neurons that control 
hand movement. 


The parietal lobe is located at the top of the brain. Neurons in the parietal 
lobe are involved in speech and also reading. Two of the parietal lobe’s 
main functions are processing somatosensation—touch sensations like 


pressure, pain, heat, cold—and processing proprioception—the sense of 
how parts of the body are oriented in space. The parietal lobe contains a 
somatosensory map of the body similar to the motor cortex. 


The occipital lobe is located at the back of the brain. It is primarily involved 
in vision—seeing, recognizing, and identifying the visual world. 


The temporal lobe is located at the base of the brain by your ears and is 
primarily involved in processing and interpreting sounds. It also contains 
the hippocampus (Greek for “seahorse”)—a structure that processes 
memory formation. The hippocampus is illustrated in [link]. The role of the 
hippocampus in memory was partially determined by studying one famous 
epileptic patient, HM, who had both sides of his hippocampus removed in 
an attempt to cure his epilepsy. His seizures went away, but he could no 
longer form new memories (although he could remember some facts from 
before his surgery and could learn new motor tasks). 


Hypothalamus 


One small but critically important part of the brain is the hypothalamus, 
shown in [link]. The hypothalamus controls the endocrine system by 
sending signals to the pituitary gland, a pea-sized endocrine gland that 
releases several different hormones that affect other glands as well as other 
cells. This relationship means that the hypothalamus regulates many 
important behaviors that are controlled by these hormones. The 
hypothalamus is the body’s thermostat—it makes sure key functions like 
food and water intake, energy expenditure, and body temperature are kept at 
appropriate levels. Neurons within the hypothalamus also regulate circadian 
rhythms, sometimes called sleep cycles. 


Cerebellum 


The cerebellum (Latin for “little brain”), shown in [link], sits at the base of 
the brain on top of the brainstem. The cerebellum controls balance and aids 
in coordinating movement and learning new motor tasks. 


Brainstem 


The brainstem, illustrated in [link], connects the rest of the brain with the 
spinal cord. It consists of the midbrain, medulla oblongata, and the pons. 
Motor and sensory neurons extend through the brainstem allowing for the 
relay of signals between the brain and spinal cord. Ascending neural 
pathways cross in this section of the brain allowing the left hemisphere of 
the cerebrum to control the right side of the body and vice versa. The 
brainstem coordinates motor control signals sent from the brain to the body. 
The brainstem controls several important functions of the body including 
alertness, arousal, breathing, blood pressure, digestion, heart rate, 
swallowing, walking, and sensory and motor information integration. 


Spinal Cord 


Connecting to the brainstem and extending down the body through the 
spinal column is the spinal cord, shown in [link]. The spinal cord is a thick 
bundle of nerve tissue that carries information about the body to the brain 
and from the brain to the body. The spinal cord is contained within the 
bones of the vertebrate column but is able to communicate signals to and 
from the body through its connections with spinal nerves (part of the 
peripheral nervous system). A cross-section of the spinal cord looks like a 
white oval containing a gray butterfly-shape, as illustrated in [link]. 
Myelinated axons make up the “white matter” and neuron and glial cell 
bodies make up the “gray matter.” Gray matter is also composed of 
interneurons, which connect two neurons each located in different parts of 
the body. Axons and cell bodies in the dorsal (facing the back of the animal) 
spinal cord convey mostly sensory information from the body to the brain. 
Axons and cell bodies in the ventral (facing the front of the animal) spinal 
cord primarily transmit signals controlling movement from the brain to the 
body. 


The spinal cord also controls motor reflexes. These reflexes are quick, 
unconscious movements—like automatically removing a hand from a hot 
object. Reflexes are so fast because they involve local synaptic connections. 
For example, the knee reflex that a doctor tests during a routine physical is 


controlled by a single synapse between a sensory neuron and a motor 
neuron. While a reflex may only require the involvement of one or two 
synapses, synapses with interneurons in the spinal column transmit 
information to the brain to convey what happened (the knee jerked, or the 
hand was hot). 


In the United States, there around 10,000 spinal cord injuries each year. 
Because the spinal cord is the information superhighway connecting the 
brain with the body, damage to the spinal cord can lead to paralysis. The 
extent of the paralysis depends on the location of the injury along the spinal 
cord and whether the spinal cord was completely severed. For example, if 
the spinal cord is damaged at the level of the neck, it can cause paralysis 
from the neck down, whereas damage to the spinal column further down 
may limit paralysis to the legs. Spinal cord injuries are notoriously difficult 
to treat because spinal nerves do not regenerate, although ongoing research 
suggests that stem cell transplants may be able to act as a bridge to 
reconnect severed nerves. Researchers are also looking at ways to prevent 
the inflammation that worsens nerve damage after injury. One such 
treatment is to pump the body with cold saline to induce hypothermia. This 
cooling can prevent swelling and other processes that are thought to worsen 
spinal cord injuries. 


White matter Gray matter 


=~ Dorsal horn 


Ventral horn 


A cross-section of the spinal 
cord shows gray matter 
(containing cell bodies and 
interneurons) and white matter 
(containing axons). 


Peripheral Nervous System 


The peripheral nervous system (PNS) is the connection between the central 
nervous system and the rest of the body. The CNS is like the power plant of 
the nervous system. It creates the signals that control the functions of the 
body. The PNS is like the wires that go to individual houses. Without those 
“wires,” the signals produced by the CNS could not control the body (and 
the CNS would not be able to receive sensory information from the body 
either). 


The PNS consists of the sensory division (afferent), which consists of 
sensory neurons, and the motor division (efferent), which consists of motor 
neurons. The sensory division conveys information to the CNS to be 
processed, and the motor division conveys the response of the CNS to 
muscles, glands and organs. The motor component of the PNS is even more 
complex and can be divided into the autonomic division and the somatic 
division. The autonomic motor division, as the name implies, is not 
controlled or initiated by the conscious thought of an individual. The 
somatic motor division is consciously controlled by the individual and 
usually affects skeletal muscles. 


Autonomic Motor Division 


Note: 


Autonomic Motor Division 


Preganglionic 
neuron: soma is / 
usually in the brain- [ 
stem or sacral 

(toward the bottom) 
spinal cord 


ganglion near the 
target organ 


Neurotransmitters 

released from 
postganglionic 

synapse: oF 
acetylcholine or nitric | 
oxide 


response is activated response is activated 


In the autonomic motor division of the 
peripheral nervous system, a preganglionic 
neuron of the CNS synapses with a 
postganglionic neuron of the PNS. The 
postganglionic neuron, in turn, acts on a target 
organ. Autonomic responses are mediated by 
the sympathetic and the parasympathetic 
systems, which are antagonistic to one another. 
The sympathetic system activates the “fight or 
flight” response, while the parasympathetic 
system activates the “rest and digest” response. 


The autonomic motor division serves as the relay between the CNS and the 
internal organs. It controls the lungs, the heart, smooth muscle, and 
exocrine and endocrine glands. The autonomic motor division controls 
these organs largely without conscious control; it can continuously monitor 
the conditions of these different systems and implement changes as needed. 
Signaling to the target tissue usually involves two synapses: a preganglionic 
neuron (originating in the CNS) synapses to a neuron in a ganglion that, in 
turn, synapses on the target organ, as illustrated in [link]. There are two 
divisions of the autonomic motor division that often have opposing effects: 
the sympathetic division and the parasympathetic division. 


Sympathetic Division 


The sympathetic division is responsible for the “fight or flight” response 
that occurs when an animal encounters a dangerous situation. One way to 
remember this is to think of the surprise a person feels when encountering a 
snake (“snake” and “sympathetic” both begin with “s”). Examples of 
functions controlled by the sympathetic division include an accelerated 
heart rate and inhibited digestion. These functions help prepare an 
organism’s body for the physical strain required to escape a potentially 
dangerous situation or to fend off a predator. 


Parasympathetic Nervous System Sympathetic Nervous System 


oS 
(NS 


Constricts pupil Dilates pupil 


Stimulates salivation Inhibits salivation 


Slows heart rate Increases heart rate 


Dilates bronchi 


Constricts bronchi 


Solar plexus Inhibits digestion 


Stimulates digestion 
Stimulates the breakdown 
of glycogen 

Stimulates bile secretion 


Stimulates secretion of 
adrenaline and noradrenaline 


Causes bladder to contract 
Inhibits contraction of bladder 


Sacral 


The sympathetic and parasympathetic divisions often have 
opposing effects on target organs. 


Most preganglionic neurons in the sympathetic division originate in the 
spinal cord, as illustrated in [link]. The axons of these neurons release 
acetylcholine on postganglionic neurons within sympathetic ganglia (the 
sympathetic ganglia form a chain that extends alongside the spinal cord). 
The acetylcholine activates the postganglionic neurons. Postganglionic 
neurons then release norepinephrine onto target organs. As anyone who 
has ever felt a rush before a big test, speech, or athletic event can attest, the 


effects of the sympathetic division are quite pervasive. This is both because 
one preganglionic neuron synapses on multiple postganglionic neurons, 
amplifying the effect of the original synapse, and because the adrenal gland 
also releases norepinephrine (and the closely related hormone epinephrine) 
into the blood stream. The physiological effects of this norepinephrine 
release include dilating the trachea and bronchi (making it easier for the 
animal to breathe), increasing heart rate, and moving blood from the skin to 
the heart, muscles, and brain (so the animal can think and run). The strength 
and speed of the sympathetic response helps an organism avoid danger. 


Parasympathetic Division 


While the sympathetic division is activated in stressful situations, the 
parasympathetic division allows an animal to “rest and digest.” One way 
to remember this is to think that during a restful situation like a picnic, the 
parasympathetic division is in control (“picnic” and “parasympathetic” both 
start with “p”). Parasympathetic preganglionic neurons have cell bodies 
located in the brainstem and in the sacral (toward the bottom) spinal cord, 
as shown in [link]. The axons of the preganglionic neurons release 
acetylcholine on the postganglionic neurons, which are generally located 
very near the target organs. Most postganglionic neurons release 
acetylcholine onto target organs, although some release nitric oxide. 


The parasympathetic division resets organ function after the sympathetic 
division is activated (the common adrenaline dump you feel after a ‘fight- 
or-flight’ event). Effects of acetylcholine release on target organs include 
slowing of heart rate, lowered blood pressure, and stimulation of digestion. 


Somatic Division 


The somatic division of the peripheral nervous system is made up of cranial 
and spinal nerves the contain motor neurons. Motor neurons transmit 
messages about desired movement from the CNS to the muscles to make 
them contract. Without its somatic division, an animal would be unable to 
process any information about its environment (what it sees, feels, hears, 


and so on) and could not control motor movements. Unlike the autonomic 
division, which has two synapses between the CNS and the target organ, 
motor neurons of the somatic division have only one synapse between the 
CNS and muscle or organ. Acetylcholine is the main neurotransmitter 
released at these synapses. 


Cranial and Spinal Nerves 


Humans have 12 cranial nerves, nerves that emerge from or enter the skull 
(cranium), as opposed to the spinal nerves, which emerge from the vertebral 
column. Each cranial nerve is accorded a name, which are detailed in [link]. 
Some cranial nerves transmit only sensory information. For example, the 
olfactory nerve transmits information about smells from the nose to the 
brainstem. Other cranial nerves transmit almost solely motor information. 
For example, the oculomotor nerve controls the opening and closing of the 
eyelid and some eye movements. Other cranial nerves contain a mix of 
sensory and motor fibers. For example, the glossopharyngeal nerve has a 
role in both taste (sensory) and swallowing (motor). 


Olfactory 
Optic 
Oculomotor 
Trochlear 


Trigeminal 


Abducens ‘ 
Facial 


Vestibulocochlear 
Glossopharyngeal 


Hypoglossal 
Vagus 


_. il —— wy 


The human brain contains 12 cranial nerves that receive 
sensory input and control motor output for the head and neck. 


Spinal nerves transmit sensory and motor information between the spinal 
cord and the rest of the body. Each of the 31 spinal nerves (in humans) 
contains both sensory and motor axons. The sensory neuron cell bodies are 
grouped in structures called dorsal root ganglia and are shown in [link]. 
Each sensory neuron has one projection—with a sensory receptor ending in 
skin, muscle, or sensory organs—and another that synapses with a neuron 
in the dorsal spinal cord. Motor neurons have cell bodies in the ventral gray 
matter of the spinal cord that project to muscle through the ventral root. 
These neurons are usually stimulated by interneurons within the spinal cord 
but are sometimes directly stimulated by sensory neurons. 


Dorsal root 


White matter e 
anglion 


Dorsal root 


Gray matter Seay 


neuron 
soma 


Motor neuron Ventral root 
soma 


Cross Section of Spinal Cord 


Spinal nerves contain both 
sensory and motor axons. The 
somas of sensory neurons are 
located in dorsal root ganglia. 

The somas of motor neurons are 
found in the ventral portion of 
the gray matter of the spinal 
cord. 


Endocrine System 


"The specific character of the greater part of the toxins which are known to 
us (I need only instance such toxins as those of tetanus and diphtheria) 
would suggest that the substances produced for effecting the corrleation of 
organs within the body, through the intermediation of the blood stream, 
might also belong to this class, since here also specificity of action must be 
a distinguishing characteristic. These chemical messengers, however, or 
"hormones"(from the Greek OppQv, to excite or arouse), as we might call 
them, have to be carried from the organ where they are produced to the 
organ which they affect by means of the blood stream, and the continually 
recurring physiological needs of the organism must determine their repeated 
production and circulation throughout the body. " Ernest Henry Starling, 
"The Chemical Correlation of the Functions of the Body", The Lancet, 
1905, II, 340 


Hormones, as Starling noted, are produced by one organ and affect the 
activities of other organs. Unlike neurotransmitters, which you will learn 
about later in this module, hormones move via the bloodstream from the 
site of production to the site of action. But like neurotransmitters, hormones 
are key players in maintaining homeostasis. Before we discuss that, 
however, we need to review homeostasis and introduce the major classes of 
animal hormones. 


Types of Hormones 


Maintaining homeostasis within the body requires the coordination of many 
different systems and organs. Communication between neighboring cells, 
and between cells and tissues in distant parts of the body, occurs through 
the release of chemicals called hormones. Hormones are chemicals that are 
released by cells into body fluids (usually blood) and which act on target 
cells at some distance from the cells that release the hormone. At the target 
cells, which are cells that have a receptor for the chemical, the hormones 
elicit a response. The cells, tissues, and organs that secrete hormones make 
up the endocrine system. Examples of glands of the endocrine system 
include the adrenal glands, which produce hormones such as epinephrine 


and norepinephrine that regulate responses to stress, and the thyroid gland, 
which produces thyroid hormones that regulate metabolic rates. 


Although there are many different hormones in the human body, they can 
be divided into two general classes based on their chemical structure and 
water solubility: steroid hormones (most are derivatives of cholesterol), 
which are not soluble in water, and peptide (peptides and proteins) 
hormones, which are readily soluble in water. One of the key distinguishing 
features of lipid-derived hormones is that they can diffuse across plasma 
membranes whereas the peptide hormones cannot. 


Lipid-Derived Hormones (or Lipid-soluble Hormones) 


Most lipid hormones are derived from cholesterol and thus are structurally 
similar to it, as illustrated in [link]. The primary class of lipid hormones in 
humans is the steroid hormones. Examples of steroid hormones include 
estradiol, which is an estrogen, or female sex hormone, and testosterone, 
which is an androgen, or male sex hormone. These two hormones are 
released by the female and male reproductive organs, respectively. Other 
steroid hormones include aldosterone and cortisol, which are released by 
the adrenal glands along with some other types of androgens. Steroid 
hormones are insoluble in water, and need to be bound to transport proteins 
in order to be transported in the blood. As a result, they remain in the body 
longer than peptide hormones. For example, cortisol has a half-life of 60 to 
90 minutes in humans, while epinephrine, an amino acid derived-hormone, 
has a half-life of approximately one minute. 


CH3 OH 


CH, 


(a) Cholesterol (b) Testosterone 


HO 
(c) Estradiol 


The structures shown here represent (a) 
cholesterol, plus the steroid hormones (b) 
testosterone and (c) estradiol. 


Peptide (water-soluble) Hormones 


The peptide hormones include polypeptides as well as several relatively 
small molecules that are derived from the amino acids tyrosine and 
tryptophan, shown in [link]. Examples of amino acid-derived hormones 
include epinephrine and norepinephrine, which are synthesized in the 
medulla of the adrenal glands, and thyroxine, which is produced by the 
thyroid gland. The pineal gland in the brain makes and secretes melatonin 
which regulates sleep cycles. 


oO OH H 

Ho ‘ 

OH cu, 
HO a HO 
Tyrosine Epinephrine 
(a) 
i | 
HN. 
NH NH2 O 
Tryptophan Melatonin 


(b) 


(a) The hormone epinephrine, which triggers 
the fight-or-flight response, is derived from the 
amino acid tyrosine. (b) The hormone 
melatonin, which regulates circadian rhythms, 
is derived from the amino acid tryptophan. 


Other peptide hormones are polypeptides (chains of amino acids linked by 
peptide bonds). These hormones include molecules that are quite short 
polypeptide chains, such as antidiuretic hormone (9 amino acids) and 
oxytocin (also 9 amino acids), both of which are produced in the brain and 
released into the blood in the posterior pituitary gland. This class also 
includes small proteins, like the growth hormones (approx 190 amino acids( 
produced by the pituitary, and large glycoproteins such as follicle- 
stimulating hormone (a complex of 2 different polypeptides, each about 100 
amino acids in length), produced by the pituitary. [link] illustrates these 
peptide hormones. 


Secreted peptides like insulin are stored within vesicles in the cells that 
synthesize them. They are then released in response to stimuli such as high 
blood glucose levels in the case of insulin. Amino acid-derived and 
polypeptide hormones are water-soluble. Therefore these hormones cannot 
cross the plasma membranes of cells; their receptors are found on the 
surface of the target cells. 


(a) (c) 


The structures of peptide hormones (a) oxytocin, (b) 
growth hormone, and (c) follicle-stimulating hormone 
are shown. These peptide hormones are much larger 
than those derived from cholesterol or amino acids. 


How Hormones Work 


Hormones mediate changes in target cells after binding to specific hormone 
receptors. In this way, even though hormones circulate throughout the body 
and come into contact with many different cell types, they only affect cells 
that possess the necessary receptors. Receptors for a specific hormone may 
be found on many different cells or may be limited to a small number of 
specialized cells. For example, thyroid hormones act on many different 
tissue types, stimulating metabolic activity throughout the body; 
testosterone receptors are found in relatively few cell types. Cells can have 
many receptors for the same hormone but often also possess receptors for 


different types of hormones. The number of receptors that respond to a 
hormone determines the cell’s sensitivity to that hormone, and the resulting 
cellular response. 


Receptor binding alters cellular activity and results in an increase or 
decrease in normal body processes. Depending on the location of the 
protein receptor on the target cell and the chemical structure of the 
hormone, hormones can mediate changes directly by binding to 
intracellular hormone receptors and modulating gene transcription, or 
indirectly by binding to cell surface receptors and stimulating signaling 
pathways. 


Intracellular Hormone Receptors 


Lipid-soluble hormones such as steroid hormones diffuse across the 
membranes of the cells where they are produced. Once outside the cell, they 
bind to transport proteins that keep them soluble in the bloodstream. At the 
target cell, the hormones are released from the carrier protein and diffuse 
across the lipid bilayer of the plasma membrane of cells. The steroid 
hormones pass through the plasma membrane of a target cell and bind to 
intracellular receptors residing in the cytoplasm or in the nucleus. The cell 
signaling pathways induced by the steroid hormones regulate specific genes 
on the cell's DNA. The hormones and receptor complex act as transcription 
regulators by increasing or decreasing the synthesis of mRNA molecules of 
specific genes. The cellular responses are varied, ranging from changes in 
the structure of the cell to the production of enzymes that catalyze new 
chemical reactions. In this way, the steroid hormone regulates specific cell 
processes as illustrated in [link]. 


PQQ PPP POP POPPI 
C0 


COQOF 
AOOOCOOOOOSOOOOOOS GAGS ALTO PPO 
SIN—“‘i‘C;:;C;O~*~*~*~*~:C~™ SS SSS 


ee f 
COTTA AS 
eT ——tit«i(‘( NOLL YY 
SALT) 
DIO IES STS 
AS Sd 
le ol by 
LN me m——‘“‘“‘“‘<‘<‘<‘<‘<i‘i‘i‘i‘“‘sSsSsSCSC*CSC SR 
OM —“————C ‘(SRST 
. 


° 

le a oe 
Rue. € FF hat 
°' 


¥ SS 89 NR dimer 
Protein 


NR/hormone 
complex Nuclear SA 
mRNA 


receptor NRIHSP ee 

C099? 200979 eeeae . 

aR) compen ATT yey eee LESOO LU Ribosome 
OOO : 


‘eo 
os hy: 


Q e 
o 
4 2 
° 
Cd 
° 


», Nuclear 
“> envelope 
D 


bh 
b 
° e. 
Mo a 
0 re, 
Chron ARE Targetgene — oth 
oF hy’ 
OieGean, © 3 9". ettt 
WOQ9e.n-.  t—‘“‘(‘(i(‘i‘itstststststS cent {J 
dhe. fe, 
IT PPP PS ocomonmenrennonOQIIITG meus 
O64 4 TT I PODOOOOOOOOOOOOOOY O, 2, 
PCOOSS 4 ¥ AVI” Cell 
COCCOCOOSOOOOOOCOOOO OF RS 
AO 
os 
COT 
COTTA 
Qutsce 
\ iJ 
BOOY 


O > 
4 COMLITVS 
° 20% 


Ud 
3 
oft, 
A 


TPO 
COG T PON. 
OGL IT P00 
OSLLIT PP O0Gge 
SLIT TPP OO QoQ oem mmecemeinoroveey 


HOO 


o J 
UO, Fee 
C55, 8) 


SALT TT YF PPP 99999909999 DOPP 
COCSG Shhh SEE T8000 


OO000000000 


An intracellular nuclear receptor (NR) is located in the 
cytoplasm bound to a heat shock protein (HSP). Upon 
hormone binding, the receptor dissociates from the heat 
shock protein and translocates to the nucleus. In the nucleus, 
the hormone-receptor complex binds to a DNA sequence 
called a hormone response element (HRE), which triggers 
gene transcription and translation. The corresponding 
protein product can then mediate changes in cell function. 


Other lipid-soluble hormones that are not steroid hormones, such as vitamin 
D and thyroxine, have receptors located in the nucleus. The hormones 
diffuse across both the plasma membrane and the nuclear envelope, then 
bind to receptors in the nucleus. The hormone-receptor complex stimulates 
transcription of specific genes. 


Plasma Membrane Hormone Receptors 


Peptide hormones are not lipid-soluble, and therefore cannot diffuse 
through the plasma membrane of cells. Lipid insoluble hormones bind to 


receptors on the outer surface of the plasma membrane. Unlike steroid 
hormones, lipid insoluble hormones do not directly affect the target cell 
because they cannot enter the cell and act directly on DNA. Binding of 
these hormones to a cell surface receptor results in activation of a signaling 
pathway; this triggers intracellular activity and carries out the specific 
effects associated with the hormone. In this way, nothing passes through the 
plasma membrane; the hormone that binds at the surface remains at the 
surface of the cell while the intracellular product remains inside the cell. 
The hormone that initiates the signaling pathway is called a first messenger, 


which activates a second messenger in the cytoplasm, as illustrated in 
[link]. 


B-Adrenergic receptor Epinephrine 


Plasma 
membrane 


The amino acid-derived hormones epinephrine and 
norepinephrine bind to beta-adrenergic receptors on the 
plasma membrane of cells. Hormone binding to receptor 
activates a G-protein, which in turn activates adenylyl 
cyclase, converting ATP to cAMP. cAMP is a second 
messenger that mediates a cell-specific response. An 
enzyme called phosphodiesterase breaks down cAMP, 
terminating the signal. 


The specific response of a cell to a lipid insoluble hormone depends on the 
type of receptors that are present on the plasma membrane and the substrate 
molecules present in the cell cytoplasm. Cellular responses to hormone 
binding of a receptor include altering membrane permeability and metabolic 
pathways, stimulating synthesis of proteins and enzymes, and activating 
hormone release. 


Hormonal Regulation of Body Systems 


Hormones have a wide range of effects and modulate many different body 
processes. Two regulatory processes that will be examined here as examples 
are regulation of the functions of the reproductive system, and regulation of 
carbohydrate metabolism. 


Hormonal Regulation of the Reproductive System 


Regulation of the reproductive system is a process that requires the action 
of hormones from the pituitary gland, the adrenal cortex, and the gonads. 
During puberty in both males and females, the hypothalamus produces 
gonadotropin-releasing hormone (GnRH), which stimulates the production 
and release of follicle-stimulating hormone (FSH) and luteinizing 
hormone (LH) from the anterior pituitary gland. These hormones regulate 
the gonads (testes in males and ovaries in females) and therefore are called 
gonadotropins. In both males and females, FSH stimulates gamete 
production and LH stimulates production of hormones by the gonads. An 
increase in gonad hormone levels inhibits GnRH production through a 
negative feedback loop. 


Regulation of the Male Reproductive System 


In males, FSH stimulates the maturation of sperm cells. FSH production is 
inhibited by the hormone inhibin, which is released by the testes. LH 


stimulates production of the sex hormones (androgens) by the interstitial 
cells of the testes and therefore is also called interstitial cell-stimulating 
hormone. 


The most widely known androgen in males is testosterone. Testosterone 
promotes the production of sperm and masculine characteristics. 


Note: 
Everyday Connection 


Professional baseball player Jason Giambi 
publically admitted to, and apologized for, 
his use of anabolic steroids supplied by a 
trainer. (credit: Bryce Edwards) 


Some athletes attempt to boost their performance by using artificial 
hormones that enhance muscle performance. Anabolic steroids, a form of 
the male sex hormone testosterone, are one of the most widely known 
performance-enhancing drugs. Steroids are used to help build muscle mass. 
Other hormones that are used to enhance athletic performance include 
erythropoietin, which triggers the production of red blood cells, and human 
growth hormone, which can help in building muscle mass. Most 
performance enhancing drugs are illegal for non-medical purposes. They 


are also banned by national and international governing bodies including 
the International Olympic Committee, the U.S. Olympic Committee, the 
National Collegiate Athletic Association, the Major League Baseball, and 
the National Football League. 

The side effects of synthetic hormones are often significant and non- 
reversible, and in some cases, fatal. Androgens produce several 
complications such as liver dysfunctions and liver tumors, prostate gland 
enlargement, difficulty urinating, premature closure of epiphyseal 
cartilages, testicular atrophy, infertility, and immune system depression. 
The physiological strain caused by these substances is often greater than 
what the body can handle, leading to unpredictable and dangerous effects 
and linking their use to heart attacks, strokes, and impaired cardiac 
function. 


Regulation of the Female Reproductive System 


In females, FSH stimulates development of egg cells, called ova, which 
develop in structures called follicles. Follicle cells produce the hormone 
inhibin, which inhibits FSH production. LH also plays a role in the 
development of ova, induction of ovulation, and stimulation of estradiol and 
progesterone production by the ovaries, as illustrated in [link]. Estradiol and 
progesterone are steroid hormones that prepare the body for pregnancy. 
Estradiol produces secondary sex characteristics in females, while both 
estradiol and progesterone regulate the menstrual cycle. 


GnRH secreted from 
the hypothalmus 
stimulates FSH 
and LH production 


Hypothalamus 


Pituitary 


in the pituitary. Estradiol, 
progesterone 
FSH and LH and inhibin are 
stimulate follicle secreted from 
growth in the ovaries. 
the ovaries. Estradiol and 
A surge in progesterone 
LH triggers regulate 
ovulation. female sex 
characteristics 
and the female 
cycle. Inhibin 


inhibits FSH 
production by 
the pituitary. 


Uterus 


Ovary 


Hormonal regulation of the 

female reproductive system 

involves hormones from the 

hypothalamus, pituitary, and 
ovaries. 


In addition to producing FSH and LH, the anterior portion of the pituitary 
gland also produces the hormone prolactin (PRL) in females. Prolactin 
stimulates the production of milk by the mammary glands following 
childbirth. Prolactin levels are regulated by the hypothalamic hormones 


prolactin-releasing hormone (PRH) and prolactin-inhibiting hormone (PIH), 
which is now known to be dopamine. PRH stimulates the release of 
prolactin and PIH inhibits it; this is a classic negative feedback loop. 


The posterior pituitary releases the hormone oxytocin, which stimulates 
uterine contractions during childbirth. The uterine smooth muscles are not 
very sensitive to oxytocin until late in pregnancy when the number of 
oxytocin receptors in the uterus peaks. Stretching of tissues in the uterus 
and cervix stimulates oxytocin release during childbirth. Contractions 
increase in intensity as blood levels of oxytocin rise via a positive feedback 
mechanism until the birth is complete. Oxytocin also stimulates the 
contraction of myoepithelial cells around the milk-producing mammary 
glands. As these cells contract, milk is forced from the secretory alveoli into 
milk ducts and is ejected from the breasts in milk ejection (“let-down’’) 
reflex. Oxytocin release is stimulated by the suckling of an infant, which 
triggers the synthesis of oxytocin in the hypothalamus and its release into 
circulation at the posterior pituitary. 


Hormonal Regulation of Carbohydrate Metabolism 


Blood glucose levels vary widely over the course of a day as periods of 
food consumption alternate with periods of fasting. Insulin and glucagon 
are the two hormones primarily responsible for maintaining homeostasis of 
blood glucose levels. Additional regulation is mediated by the thyroid 
hormones. 


Regulation of Blood Glucose Levels by Insulin and Glucagon 


Cells of the body require nutrients in order to function, and these nutrients 
are obtained through feeding. In order to manage nutrient intake, storing 
excess intake and utilizing reserves when necessary, the body uses 
hormones to moderate energy stores. Insulin is produced by the beta cells 
of the pancreas, which are stimulated to release insulin as blood glucose 
levels rise (for example, after a meal is consumed). Insulin lowers blood 
glucose levels by enhancing the rate of glucose uptake and utilization by 


target cells, which use glucose for ATP production. It also stimulates the 
liver to convert glucose to glycogen, which is then stored by cells for later 
use. Insulin also increases glucose transport into certain cells, such as 
muscle cells, fat cells, and liver cells. This results from an insulin-mediated 
increase in the number of glucose transporter proteins in plasma 
membranes, which remove glucose from circulation by facilitated diffusion. 
As insulin binds to its target cell via insulin receptors and signal 
transduction, it triggers the cell to incorporate glucose transport proteins 
into its membrane. Insulin also stimulates the conversion of glucose to fat in 
adipocytes and the synthesis of proteins. These actions mediated by insulin 
cause blood glucose concentrations to fall, called a hypoglycemic “low 
sugar” effect, which inhibits further insulin release from beta cells through a 
negative feedback loop. 


When blood glucose levels decline below normal levels, for example 
between meals or when glucose is utilized rapidly during exercise, the 
hormone glucagon is released from the alpha cells of the pancreas. 
Glucagon raises blood glucose levels, eliciting what is called a 
hyperglycemic effect, by stimulating the breakdown of glycogen to glucose 
in skeletal muscle cells and liver cells in a process called glycogenolysis. 
Glucose can then be utilized as energy by muscle cells and released into 
circulation by the liver cells. Glucagon also stimulates absorption of amino 
acids from the blood by the liver, which then converts them to glucose. This 
process of glucose synthesis is called gluconeogenesis. Glucagon also 
stimulates adipose cells to release fatty acids into the blood. These actions 
mediated by glucagon result in an increase in blood glucose levels to 
normal homeostatic levels. Rising blood glucose levels inhibit further 
glucagon release by the pancreas via a negative feedback mechanism. In 
this way, insulin and glucagon work together to maintain homeostatic 
glucose levels, as shown in [Link]. 


(” ‘N 
‘| 


Y 


XN / 


Insulin and glucagon regulate blood glucose levels via 
negative feedback mechanisms. 


Impaired insulin function can lead to a condition called diabetes mellitus, 
the main symptoms of which are illustrated in [link]. This can be caused by 
low levels of insulin production by the beta cells of the pancreas, or by 
reduced sensitivity of tissue cells to insulin. This prevents glucose from 
being absorbed by cells, causing high levels of blood glucose, or 
hyperglycemia (high sugar). High blood glucose levels make it difficult for 
the kidneys to recover all the glucose from nascent urine, resulting in 
glucose being lost in urine. High glucose levels also result in less water 
being reabsorbed by the kidneys, causing high amounts of urine to be 
produced; this may result in dehydration. Over time, high blood glucose 
levels can cause nerve damage to the eyes and peripheral body tissues, as 
well as damage to the kidneys and cardiovascular system. Oversecretion of 
insulin can cause hypoglycemia, low blood glucose levels. This causes 


insufficient glucose availability to cells, often leading to muscle weakness, 
and can sometimes cause unconsciousness or death if left untreated. 


Central nervous 
system 

* Lethargy 

* Stupor 

* Excessive thirst 
* Excessive hunger 


Eyes 
Blurred vision 


Breath 
Systemic + Smell of acetone 


* Weight loss 


Gastric 

+ Nausea 

+ Vomiting 

+ Abdominal 
pain 


Urinary 
* Frequent 
urination 
_ Glucose 
In urine 
The main symptoms of 
diabetes are shown. (credit: 


modification of work by 
Mikael Haggstr6m) 


Respiratory 
* Hyperventilati 


Endocrine Glands 


Both the endocrine and nervous systems use chemical signals to 
communicate and regulate the body's physiology. The endocrine system 
releases hormones that act on target cells to regulate development, growth, 
energy metabolism, reproduction, and many behaviors. The nervous system 
releases neurotransmitters or neurohormones that regulate neurons, muscle 
cells, and endocrine cells. Because the neurons can regulate the release of 
hormones, the nervous and endocrine systems work in a coordinated 
manner to regulate the body's physiology. 


Hypothalamic-Pituitary Axis 


The hypothalamus in vertebrates integrates the endocrine and nervous 
systems. The hypothalamus is an endocrine organ located in the 
diencephalon of the brain. It receives input from the body and other brain 
areas and initiates endocrine responses to environmental changes. The 
hypothalamus acts as an endocrine organ, synthesizing hormones and 
transporting them along axons to the posterior pituitary gland. It synthesizes 
and secretes regulatory hormones that control the endocrine cells in the 
anterior pituitary gland. The hypothalamus contains autonomic centers that 
control endocrine cells in the adrenal medulla via neuronal control. 


The pituitary gland, sometimes called the hypophysis or “master gland” is 
located at the base of the brain in the sella turcica, a groove of the sphenoid 
bone of the skull, illustrated in [link]. It is attached to the hypothalamus via 
a stalk called the pituitary stalk (or infundibulum). The anterior portion of 
the pituitary gland is regulated by releasing or release-inhibiting hormones 
produced by the hypothalamus, and the posterior pituitary receives signals 
via neurosecretory cells to release hormones produced by the 
hypothalamus. The pituitary has two distinct regions—the anterior pituitary 
and the posterior pituitary—which between them secrete nine different 
peptide or protein hormones. The posterior lobe of the pituitary gland 
contains axons of the hypothalamic neurons. 


\ Ma Pituitary stalk 
Cerebellum An = == oN 
iy } . \ 


Hypothalamus 
Brain stem 


———— Spinal cord Anterior pituitary Posterior pituitary 


(a) (b) 


The pituitary gland is located at (a) the base of the brain 
and (b) connected to the hypothalamus by the pituitary 


stalk. (credit a: modification of work by NCI; credit b: 
modification of work by Gray’s Anatomy) 


Thyroid Gland 


The thyroid gland is located in the neck, just below the larynx and in front 
of the trachea, as shown in [link]. It is a butterfly-shaped gland with two 
lobes that are connected by the isthmus. It has a dark red color due to its 
extensive vascular system. When the thyroid swells due to dysfunction, it 
can be felt under the skin of the neck. 


Thyroid gland 


Trachea 


This illustration shows the 
location of the thyroid 
gland. 


Thyroid follicle cells synthesize the hormone thyroxine, which is also 
known as Ty because it contains four atoms of iodine, and triiodothyronine, 
also known as T3 because it contains three atoms of iodine. Follicle cells are 


stimulated to release stored T3 and Ty, by thyroid stimulating hormone 
(TSH), which is produced by the anterior pituitary. These thyroid hormones 
increase the rates of mitochondrial ATP production. 


A third hormone, calcitonin, is produced by parafollicular cells of the 
thyroid either releasing hormones or inhibiting hormones. Calcitonin 
release is not controlled by TSH, but instead is released when calcium ion 
concentrations in the blood rise. Calcitonin functions to help regulate 
calcium concentrations in body fluids. It acts in the bones to inhibit 
osteoclast activity and in the kidneys to stimulate excretion of calcium. The 
combination of these two events lowers body fluid levels of calcium. 


Parathyroid Glands 


Most people have four parathyroid glands; however, the number can vary 
from two to six. These glands are located on the posterior surface of the 
thyroid gland, as shown in [link]. Normally, there is a superior gland and an 
inferior gland associated with each of the thyroid’s two lobes. Each 
parathyroid gland is covered by connective tissue and contains many 
secretory cells that are associated with a capillary network. 


— Thyroid gland 


Parathyroid gland 


The parathyroid glands are 


located on the posterior of the 
thyroid gland. (credit: 
modification of work by 
NCI) 


The parathyroid glands produce parathyroid hormone (PTH). PTH increases 
blood calcium concentrations when calcium ion levels fall below normal. 
PTH (1) enhances reabsorption of Ca** by the kidneys, (2) stimulates 
osteoclast activity and inhibits osteoblast activity, and (3) it stimulates 
synthesis and secretion of calcitriol by the kidneys, which enhances Ca?* 
absorption by the digestive system. PTH and calcitonin work in opposition 
to one another to maintain homeostatic Ca** levels in body fluids. 


Adrenal Glands 


The adrenal glands are associated with the kidneys; one gland is located on 
top of each kidney as illustrated in [link]. The adrenal glands consist of an 
outer adrenal cortex and an inner adrenal medulla. These regions secrete 
different hormones. 


Adrenal gland 


Kidney 


The location of the adrenal 
glands on top of the kidneys 
is shown. (credit: 
modification of work by 
NCI) 


Adrenal Cortex 


The adrenal cortex is made up of layers of epithelial cells and associated 
capillary networks. This gland produces mineralcorticoids, glucocorticoids, 
and androgens. The main mineralocorticoid (a class of steroid hormones 
that regulate salt and water balance) is aldosterone, which regulates the 
concentration of Na”* ions in urine, sweat, pancreas, and saliva. Aldosterone 
release from the adrenal cortex is stimulated by a decrease in blood 
concentrations of sodium ions, blood volume, or blood pressure, or by an 
increase in blood potassium levels. 


The three main glucocorticoids (steroid hormones that regulate glucose 
metabolism) are cortisol, corticosterone, and cortisone. The glucocorticoids 
stimulate the synthesis of glucose. and can also enhance gluconeogenesis 
(conversion of a non-carbohydrate to glucose) by liver cells. They also 
promote the release of fatty acids from adipose tissue. These hormones 
increase blood glucose levels to maintain levels within a normal range 
between meals. These hormones are secreted in response to ACTH, and 
levels are regulated by negative feedback. 


Androgens are sex hormones that promote masculinity. They are produced 
in small amounts by the adrenal cortex in both males and females. They do 
not affect sexual characteristics and may supplement sex hormones released 
from the gonads. 


Adrenal Medulla 


The adrenal medulla contains two types of secretory cells: one that 
produces epinephrine (adrenaline) and another that produces norepinephrine 
(noradrenaline). Epinephrine is the primary adrenal medulla hormone 
accounting for 75 to 80 percent of its secretions. Epinephrine and 
norepinephrine increase heart rate, breathing rate, cardiac muscle 
contractions, blood pressure, and blood glucose levels. They also accelerate 
the breakdown of glucose in skeletal muscles and stored fats in adipose 
tissue. 


The release of epinephrine and norepinephrine is stimulated by neural 
impulses from the sympathetic nervous system. Neural impulses, 
originating from the hypothalamus in response to stress, release these 
hormones to prepare the body for the fight-or-flight response. 


Pancreas 


The pancreas, illustrated in [link], is an elongated organ that is located 
between the stomach and the proximal portion of the small intestine. It 
contains both exocrine cells that excrete digestive enzymes and endocrine 
cells that release hormones. It is sometimes referred to as a heterocrine 
gland because it has both endocrine and exocrine functions. 


Stomach 


Gall bladder 


Common bile duct 


Duodenum Pancreas 


The pancreas is found 
underneath the stomach and 
points toward the spleen. 
(credit: modification of work 
by NCI) 


The endocrine cells of the pancreas form clusters called pancreatic islets or 
the islets of Langerhans, as visible in the micrograph shown in [link]. The 
pancreatic islets contain two primary cell types: alpha cells, which produce 
the hormone glucagon, and beta cells, which produce the hormone insulin. 
These hormones regulate blood glucose levels. As blood glucose levels 
decline, alpha cells release glucagon to raise the blood glucose levels by 
increasing rates of glycogen breakdown and glucose release by the liver. 
When blood glucose levels rise, such as after a meal, beta cells release 
insulin to lower blood glucose levels by increasing the rate of glucose 
uptake in most body cells, and by increasing glycogen synthesis in skeletal 
muscles and the liver. Together, glucagon and insulin regulate blood 
glucose levels. 


The islets of Langerhans are 
clusters of endocrine cells 
found in the pancreas; they 

stain lighter than surrounding 

cells. (credit: modification of 


work by Muhammad T. Tabiin, 
Christopher P. White, Grant 
Morahan, and Bernard E. Tuch; 
scale-bar data from Matt 
Russell) 


Pineal Gland 


The pineal gland produces melatonin. The rate of melatonin production is 
affected by the photoperiod (amount of light in a 24-hour period). Nerves 
from the visual pathways innervate the pineal gland. During the day (light), 
little melatonin is produced; however, melatonin production increases 
during the night (dark). In some mammals, melatonin has an inhibitory 
affect on reproductive functions by decreasing production and maturation of 
sperm, oocytes, and reproductive organs. Lastly, melatonin is involved in 
biological rhythms, particularly circadian rhythms such as the sleep-wake 
cycle and eating habits. 


Gonads 


The gonads—the male testes and female ovaries—produce steroid 
hormones. The testes produce androgens, testosterone being the most 
prominent, which allow for the development of secondary sex 
characteristics and the production of sperm cells. The ovaries produce 
estradiol and progesterone, which cause secondary sex characteristics and 
prepare the body for childbirth. 


Endocrine Glands and their Associated Hormones 


Endocrine 
Gland 


Hypothalamus 


Pituitary 
(Anterior) 


Associated 
Hormones 


releasing and 
inhibiting 
hormones 


antidiuretic 
hormone (ADH) 


growth hormone 
(GH) 


prolactin (PRL) 


thyroid stimulating 
hormone (TSH) 


adrenocorticotropic 
hormone (ACTH) 


follicle-stimulating 
hormone (FSH) 


Effect 


regulate hormone release 
from pituitary gland; 
produce oxytocin; 
produce uterine 
contractions and milk 
secretion in females 


water reabsorption from 
kidneys; vasoconstriction 
to increase blood 
pressure 


promotes growth of body 
tissues, protein synthesis; 
metabolic functions 


promotes milk 
production 


stimulates thyroid 
hormone release 


stimulates hormone 
release by adrenal 
cortex, glucocorticoids 


stimulates gamete 
production (both ova and 
sperm); secretion of 
estradiol 


Endocrine Glands and their Associated Hormones 


Endocrine 
Gland 


Pituitary 
(Posterior) 


Thyroid 


Parathyroid 


Associated 
Hormones 


luteinizing 
hormone (LH) 


melanocyte- 
stimulating 
hormone (MSH) 


antidiuretic 
hormone (ADH) 


oxytocin 


thyroxine, 
triiodothyronine 


calcitonin 


parathyroid 
hormone (PTH) 


Effect 


stimulates androgen 
production by gonads; 
ovulation, secretion of 
progesterone 


stimulates melanocytes 
of the skin increasing 
melanin pigment 
production. 


stimulates water 
reabsorption by kidneys 


stimulates uterine 
contractions during 
childbirth; milk ejection; 
stimulates ductus 
deferens and prostate 
gland contraction during 
emission 


stimulate and maintain 
metabolism; growth and 
development 


reduces blood Ca2* 
levels 


increases blood Ca2* 
levels 


Endocrine Glands and their Associated Hormones 


Endocrine 
Gland 


Adrenal 
(Cortex) 


Adrenal 
(Medulla) 


Pancreas 


Pineal gland 


Testes 


Associated 
Hormones 


aldosterone 


cortisol, 
corticosterone, 
cortisone 


epinephrine, 
norepinephrine 


insulin 


glucagon 


melatonin 


androgens 


Effect 


increases blood Na* 
levels; increase K* 
secretion 


increase blood glucose 
levels; anti-inflammatory 
effects 


stimulate fight-or-flight 
response; increase blood 
gluclose levels; increase 
metabolic activities 


reduces blood glucose 
levels 


increases blood glucose 
levels 


regulates some 
biological rhythms and 
protects CNS from free 
radicals 


regulate, promote, 
increase or maintain 
sperm production; male 
secondary sexual 
characteristics 


Endocrine Glands and their Associated Hormones 


Endocrine Associated 
Gland Hormones Effect 
promotes uterine lining 
growth; female 
estrogen 
secondary sexual 
Ovaries characteristics 
promote and maintain 
progestins 


uterine lining growth 


Digestive System Regulation 


Introduction 

"The digestive canal is in its task a complete chemical factory. The raw 
material passes through a long series of institutions in which it is subjected 
to certain mechanical and, mainly, chemical processing, and then, through 
innumerable side-streets, it is brought into the depot of the body. Aside 
from this basic series of institutions, along which the raw material moves, 
there is a series of lateral chemical manufactories, which prepare certain 
reagents for the appropriate processing of the raw material." Ivan Petrovich 
Pavlov, Speech to the Society of Russian Physicians, Dec. 1874 


Pavlov's pioneering work, showing that dogs can associate the ringing of a 
bell with the imminent delivery of food, pointed the way toward our current 
understanding of the coordinated responses that regulate the digestive 
system. The brain is the control center for the sensation of hunger and 
satiety. The functions of the digestive system are regulated through neural 
and hormonal responses. 


Neural Responses to Food 


In reaction to the smell, sight, or thought of food, like that shown in [link], 
the first hormonal response is that of salivation. The salivary glands secrete 
more saliva in response to the stimulus presented by food in preparation for 
digestion. Simultaneously, the stomach begins to produce hydrochloric acid 
to digest the food. Recall that the peristaltic movements of the esophagus 
and other organs of the digestive tract are under the control of the brain. 
The brain prepares these muscles for movement as well. When the stomach 
is full, the part of the brain that detects satiety signals fullness. There are 
three overlapping phases of gastric control—the cephalic phase, the gastric 
phase, and the intestinal phase—each requires many enzymes and is under 
neural control as well. 


Seeing a plate of food triggers the 
secretion of saliva in the mouth and 
the production of HCL in the stomach. 
(credit: Kelly Bailey) 


Digestive Phases 


The response to food begins even before food enters the mouth. The first 
phase of ingestion, called the cephalic phase, is controlled by the neural 
response to the stimulus provided by food. All aspects—such as sight, 
sense, and smell—trigger the neural responses resulting in salivation and 
secretion of gastric juices. The gastric and salivary secretion in the cephalic 
phase can also take place due to the thought of food. Right now, if you think 
about a piece of chocolate or a crispy potato chip, the increase in salivation 
is a cephalic phase response to the thought. The central nervous system 
prepares the stomach to receive food. 


The gastric phase begins once the food arrives in the stomach. It builds on 
the stimulation provided during the cephalic phase. Gastric acids and 
enzymes process the ingested materials. The gastric phase is stimulated by 


(1) distension of the stomach, (2) a decrease in the pH of the gastric 
contents, and (3) the presence of undigested material. This phase consists of 
local, hormonal, and neural responses. These responses stimulate secretions 
and powerful contractions. 


The intestinal phase begins when chyme enters the small intestine 
triggering digestive secretions. This phase controls the rate of gastric 
emptying. In addition to gastric emptying, when chyme enters the small 
intestine, it triggers other hormonal and neural events that coordinate the 
activities of the intestinal tract, pancreas, liver, and gallbladder. 


Hormonal Responses to Food 


The endocrine system controls the response of the various glands in the 
body and the release of hormones at the appropriate times. 


One of the important factors under hormonal control is the stomach acid 
environment. During the gastric phase, the hormone gastrin is secreted by 
G cells in the stomach in response to the presence of proteins in the 
stomach contents. Gastrin stimulates the release of hydrochloric acid (HCl), 
which aids in the digestion of the proteins. However, when the stomach is 
emptied, the acidic environment no longer needs to be maintained, and a 
hormone called somatostatin stops the release of hydrochloric acid. This is 
a good example of a negative feedback system: proteins in the stomach 
cause a response that results in elimination of proteins from the stomach 
contents, via the actions of two counteracting hormones. 


In the duodenum, digestive secretions from the liver, pancreas, and 
gallbladder play an important role in digesting chyme during the intestinal 
phase. In order to neutralize the acidic chyme, a hormone called secretin 
stimulates the pancreas to produce alkaline bicarbonate solution and deliver 
it to the duodenum. Secretin acts in tandem with another hormone called 
cholecystokinin (CCK). Not only does CCK stimulate the pancreas to 
produce the requisite pancreatic juices, it also stimulates the gallbladder to 
release bile into the duodenum. This is another negative feedback loop; 
what parameters are being sensed and regulated? 


Another level of hormonal control occurs in response to the composition of 
food. Foods high in lipids take a long time to digest. A hormone called 
gastric inhibitory peptide is secreted by the small intestine to slow down the 
peristaltic movements of the intestine to allow fatty foods more time to be 
digested and absorbed. 


Understanding the hormonal control of the digestive system is an important 
area of ongoing research. Scientists are exploring the role of each hormone 
in the digestive process and developing ways to target these hormones. 
Advances could lead to knowledge that may help to battle the obesity 
epidemic. 


How Animals Reproduce 


Introduction 

" Reproduction is so primitive and fundamental a function of vital 
organisms that the mechanism by which it is assured is highly complex and 
not yet clearly understood. It is not necessarily connected with sex, nor is 
sex necessarily connected with reproduction." Henry Havelock Ellis, in 
Psychology of Sex, 1933 


Some animals produce offspring through asexual reproduction while other 
animals produce offspring through sexual reproduction. Both methods have 
advantages and disadvantages. Asexual reproduction produces offspring 
that are genetically identical to the parent because the offspring are all 
clones of the original parent. A single individual can produce offspring 
asexually and large numbers of offspring can be produced quickly; these are 
two advantages that asexually reproducing organisms have over sexually 
reproducing organisms. In a stable or predictable environment, asexual 
reproduction is an effective means of reproduction because all the offspring 
will be adapted to that environment. In an unstable or unpredictable 
environment, species that reproduce asexually may be at a disadvantage 
because all the offspring are genetically identical and may not be adapted to 
different conditions. 


During sexual reproduction, the genetic material of two individuals is 
combined to produce genetically diverse offspring that differ from their 
parents. The genetic diversity of sexually produced offspring is thought to 
give sexually reproducing individuals greater fitness because more of their 
offspring may survive and reproduce in an unpredictable or changing 
environment. Species that reproduce sexually (and have separate sexes) 
must maintain two different types of individuals, males and females. Only 
half the population (females) can produce the offspring, so fewer offspring 
will be produced when compared to asexual reproduction. This is a 
disadvantage of sexual reproduction compared to asexual reproduction. 


Asexual Reproduction 


Asexual reproduction occurs in prokaryotic microorganisms (bacteria and 
archaea) and in many eukaryotic, single-celled and multi-celled organisms, 
both plants and animals. There are several ways that animals reproduce 
asexually, the details of which vary among individual species. 


Fission 


Fission, also called binary fission, occurs in some invertebrate, multi-celled 
organisms. It is in some ways analogous to the process of binary fission of 
single-celled prokaryotic organisms. The term fission is applied to instances 
in which an organism appears to split itself into two parts and, if necessary, 
regenerate the missing parts of each new organism. For example, some 
flatworms, such as Dugesia dorotocephala, are able to separate their bodies 
into head and tail regions and then regenerate the missing half in each of the 
two new organisms. Sea anemones (Cnidaria), such as species of the genus 
Anthopleura ({link]), will divide along the oral-aboral axis, and sea 
cucumbers (Echinodermata) of the genus Holothuria, will divide into two 
halves across the oral-aboral axis and regenerate the other half in each of 
the resulting individuals. 


The Anthopleura artemisia 
sea anemone can reproduce 
through fission. 


Budding 


Budding is a form of asexual reproduction that results from the outgrowth 
of a part of the body leading to a separation of the “bud” from the original 
organism and the formation of two individuals, one smaller than the other. 
Budding occurs commonly in some invertebrate animals such as hydras and 
corals. In hydras, a bud forms that develops into an adult and breaks away 
from the main body ([link]). 


(a) Hydra reproduce asexually through 
budding: a bud forms on the tubular body of an 
adult hydra, develops a mouth and tentacles, 
and then detaches from its parent. The new 
hydra is fully developed and will find its own 
location for attachment. (b) Some coral, such 
as the Lophelia pertusa shown here, can 
reproduce through budding. (credit b: 
modification of work by Ed Bowlby, 
NOAA/Olympic Coast NMS; 
NOAA/OAR/Office of Ocean Exploration) 


Fragmentation 


Fragmentation is the breaking of an individual into parts followed by 
regeneration. If the animal is capable of fragmentation, and the parts are big 
enough, a separate individual will regrow from each part. Fragmentation 
may occur through accidental damage, damage from predators, or as a 
natural form of reproduction. Reproduction through fragmentation is 
observed in sponges, some cnidarians, turbellarians, echinoderms, and 
annelids. In some sea stars, a new individual can be regenerated from a 
broken arm and a piece of the central disc. This sea star ({link]) is in the 
process of growing a complete sea star from an arm that has been cut off. 
Fisheries workers have been known to try to kill the sea stars eating their 
clam or oyster beds by cutting them in half and throwing them back into the 
ocean. Unfortunately for the workers, the two parts can each regenerate a 
new half, resulting in twice as many Sea stars to prey upon the oysters and 
clams. 


(b) 


(a) Linckia multifora is a species of sea star 
that can reproduce asexually via fragmentation. 
In this process, (b) an arm that has been shed 
grows into a new Sea Star. (credit a: 
modifiction of work by Dwayne Meadows, 
NOAA/NMEFS/OPR) 


Parthenogenesis 


Parthenogenesis is a form of asexual reproduction in which an egg 
develops into an individual without being fertilized. The resulting offspring 
can be either haploid or diploid, depending on the process and the particular 
species. Parthenogenesis occurs in invertebrates such as water fleas, 
rotifers, aphids, stick insects, and ants, wasps, and bees. Ants, bees, and 
wasps use parthenogenesis to produce haploid males (drones). The diploid 
females (workers and queens) are the result of a fertilized egg. 


Some vertebrate animals—including some reptiles, amphibians, and fish— 
also reproduce through parthenogenesis. Parthenogenesis has been observed 
in species in which the sexes were separated in terrestrial or marine zoos. 
Two female Komodo dragons, a hammerhead shark, and a blacktop shark 
have produced parthenogenic young, even when the females have been 
isolated from males. It is possible that these instances of parthenogenesis 
occurred in response to unusual circumstances stemming from captivity, 
and would normally not occur. 


Sexual Reproduction 


Sexual reproduction is the combination of reproductive cells from two 
individuals, each contributing a haploid gamete, to generate genetically 
unique offspring. The nature of the individuals that produce the two kinds 
of gametes can vary, having for example separate sexes or both sexes in 
each individual. 


Hermaphroditism 


Hermaphroditism occurs in animals in which one individual has both male 
and female reproductive systems. Invertebrates such as earthworms, slugs, 
tapeworms, and snails ([link]) are often hermaphroditic. Hermaphrodites 


may self-fertilize, but typically they will mate with another of their species, 
fertilizing each other and both producing offspring. Self-fertilization is 
more common in animals that have limited mobility or are not motile, such 
as barnacles and clams. Many species have specific mechanisms in place to 
prevent self-fertilization, because it is an extreme form of inbreeding and 
usually produces less fit offspring. 


Many (a) snails are hermaphrodites. When two 
individuals (b) mate, they can produce up to 
100 eggs each. (credit a: modification of work 
by Assaf Shtilman; credit b: modification of 
work by "Schristia"/Flickr) 


Fertilization 


The fusion of a sperm and an egg is a process called fertilization. This can 
occur either inside (internal fertilization) or outside (external fertilization) 
the body of the female. Humans provide an example of the former, whereas 
frog reproduction is an example of the latter. 


External Fertilization 


External fertilization usually occurs in aquatic environments where both 
eggs and sperm are released into the water. After the sperm reaches the egg, 
fertilization takes place. Most external fertilization happens during the 
process of spawning where one or several females release their eggs and the 
male(s) release sperm in the same area, at the same time. The spawning 
may be triggered by environmental signals, such as water temperature or 
the length of daylight. Nearly all fish spawn, as do crustaceans (such as 
crabs and shrimp), mollusks (such as oysters), squid, and echinoderms 
(such as sea urchins and sea cucumbers). Frogs, corals, mayflies, and 
mosquitoes also spawn ((link]). 


During sexual reproduction in 
toads, the male grasps the female 
from behind and externally 
fertilizes the eggs as they are 
deposited. (credit: Bernie Kohl) 


Internal Fertilization 


Internal fertilization occurs most often in terrestrial animals, although some 
aquatic animals also use this method. Internal fertilization may occur by the 
male directly depositing sperm in the female during mating. It may also 
occur by the male depositing sperm in the environment, usually in a 


protective structure, which a female picks up to deposit the sperm in her 
reproductive tract. There are three ways that offspring are produced 
following internal fertilization. In oviparity, fertilized eggs are laid outside 
the female’s body and develop there, receiving nourishment from the yolk 
that is a part of the egg ([link]a). This occurs in insects, some bony fish, 
some reptiles, a few cartilaginous fish, some amphibians, a few mammals, 
and all birds. Most non-avian reptiles and insects produce leathery eggs, 
while birds and some turtles produce eggs with high concentrations of 
calcium carbonate in the shell, making them hard. Chicken eggs are an 
example of a hard shell. The eggs of the egg-laying mammals such as the 
platypus and echidna are leathery. 


In ovoviparity, fertilized eggs are retained in the female, and the embryo 
obtains its nourishment from the egg’s yolk. The eggs are retained in the 
female’s body until they hatch inside of her, or she lays the eggs right 
before they hatch. This process helps protect the eggs until hatching. This 
occurs in some bony fish (like the platyfish Xiphophorus maculatus, 
[link]b), some sharks, lizards, some snakes (garter snake Thamnophis 
sirtalis), Some vipers, and some invertebrate animals (Madagascar hissing 
cockroach Gromphadorhina portentosa). 


In viviparity the young are born alive. They obtain their nourishment from 
the female and are born in varying states of maturity. This occurs in most 
mammals ([link]c), some cartilaginous fish, and a few reptiles. 


(a) (b) (c) 


In (a) oviparity, young develop in eggs outside the 
female body, as with these Harmonia axydridis beetles 
hatching. Some aquatic animals, like this (b) pregnant 


Xiphophorus maculatus are ovoviparous, with the egg 
developing inside the female and nutrition supplied 
primarily from the yolk. In mammals, nutrition is 
supported by the placenta, as was the case with this (c) 
newborn squirrel. (credit b: modification of work by 
Gourami Watcher; credit c: modification of work by 
"audreyjm529"/Flickr) 


Hormonal Control of Reproduction 


In the animal kingdom there are many interesting examples of reproductive 
strategies, and hormones are involved in regulating all of those. Rather than 
attempt to cover the wide diversity of strategies and hormones, we will 
concentrate on the hormonal control of reproduction in a single species, 
Homo sapiens. 


The human male and female reproductive cycles are controlled by the 
interaction of hormones from the hypothalamus and anterior pituitary with 
hormones from reproductive tissues and organs. In both sexes, the 
hypothalamus monitors and causes the release of hormones from the 
anterior pituitary gland. When the reproductive hormone is required, the 
hypothalamus sends a gonadotropin-releasing hormone (GnRH) to the 
anterior pituitary. This causes the release of follicle stimulating hormone 
(FSH) and luteinizing hormone (LH) from the anterior pituitary into the 
blood. Although these hormones are named after their functions in female 
reproduction, they are produced in both sexes and play important roles in 
controlling reproduction. Other hormones have specific functions in the 
male and female reproductive systems. 


Male Hormones 


At the onset of puberty, the hypothalamus causes the release of FSH and 
LH into the male system for the first time. FSH enters the testes and 


stimulates the Sertoli cells located in the walls of the seminiferous tubules 
to begin promoting spermatogenesis ([link]). LH also enters the testes and 
stimulates the interstitial cells of Leydig, located in between the walls of the 
seminiferous tubules, to make and release testosterone into the testes and 
the blood. 


Testosterone stimulates spermatogenesis. This hormone is also responsible 
for the secondary sexual characteristics that develop in the male during 
adolescence. The secondary sex characteristics in males include a 
deepening of the voice, the growth of facial, axillary, and pubic hair, an 
increase in muscle bulk, and the beginnings of the sex drive. 


Pituitary hormone effects: [Hypothalamus | 
LH and FSH stimulate spermatogenesis 


and testosterone secretion by the testes. y GnRH 


Inhibin 
Testosterone 


Se oe Nate Testes hormone effects: 
Bete oe Testosterone and inhibin inhibit 
the secretion of GnRH by the 
Leydig cells hypothalamus and LH and FSH 
by the pituitary. 


Hormones control sperm production in a negative feedback 
system. 


LH 


A negative feedback system occurs in the male with rising levels of 
testosterone acting on the hypothalamus and anterior pituitary to inhibit the 
release of GnRH, FSH, and LH. In addition, the Sertoli cells produce the 
hormone inhibin, which is released into the blood when the sperm count is 
too high. This inhibits the release of GnRH and FSH, which will cause 
spermatogenesis to slow down. If the sperm count reaches a low of 20 
million/mL, the Sertoli cells cease the release of inhibin, and the sperm 
count increases. 


Female Hormones 


The control of reproduction in females is more complex. The female 
reproductive cycle is divided into the ovarian cycle and the menstrual cycle. 
The ovarian cycle governs the preparation of endocrine tissues and release 
of eggs, while the menstrual cycle governs the preparation and maintenance 
of the uterine lining ({link]). These cycles are coordinated over a 22—32 day 
cycle, with an average length of 28 days. 


As with the male, the GnRH from the hypothalamus causes the release of 
the hormones FSH and LH from the anterior pituitary. In addition, estrogen 
and progesterone are released from the developing follicles. As with 
testosterone in males, estrogen is responsible for the secondary sexual 
characteristics of females. These include breast development, flaring of the 
hips, and a shorter period for bone growth. 


The Ovarian Cycle and the Menstrual Cycle 


The ovarian and menstrual cycles are regulated by hormones of the 
hypothalamus, pituitary, and ovaries ([link]). The ebb and flow of the 
hormones causes the ovarian and menstrual cycles to advance. The ovarian 
and menstrual cycles occur concurrently. The first half of the ovarian cycle 
is the follicular phase. Slowly rising levels of FSH cause the growth of 
follicles on the surface of the ovary. This process prepares the egg for 
ovulation. As the follicles grow, they begin releasing estrogen. The first few 
days of this cycle coincide with menstruation or the sloughing off of the 
functional layer of the endometrium in the uterus. After about five days, 
estrogen levels rise and the menstrual cycle enters the proliferative phase. 
The endometrium begins to regrow, replacing the blood vessels and glands 
that deteriorated during the end of the last cycle. 


| Follicular phase Il Ovulation 

Pituitary hormone Pituitary hormone 

effect: LH and FSH effect: LH and FSH 

stimulate several GnRH stimulate maturation GnRH 
follicles to grow. of one of the 


growing follicles. 


Estrogen 


Ovarian Ovarian 
hormone hormone 
effects: effects: 


Dominant follicle 

produces low 

levels of estrogen, 

which: 

e Stimulate GnRH 
secretion by the 
hypothalamus. 


FSH Follicles produce 
low levels of 


FSH 
H estrogen that LH 
Estrogen inhibit GaRH 
secretion by 
| Fotis | the hypothalamus, 
keeping LH and 
FSH levels low. LH and FSH 


Estrogen Cause endometrial Estrogen _ levels rise, 
arteries to constrict resulting in 
due to low levels, ovulation about 
resulting in a day later. 

endometium| menstruation. endometium| e Cause the 
endometrium 


to thicken. 


Ill Luteal phase 


Pituitary hormone 
effect: LH stimulates 
formation of a corpus GnRH 
luteum from follicular 
tissue left behind after 
ovulation. 


Ovarian 
hormone 
effects: 

The corpus 
luteum secretes 


LH Zp 
Progesterone estrogen and 
progesterone that 
Corpus luteum e Block GnRH 


production by the 
hypothalamus 
Estrogen and LH and 


| FSH production 
Progesterone by the pituitary. 
aa Cause the 
| Endometium | endometrium to 
further develop. 


The ovarian and menstrual cycles of female reproduction 
are regulated by hormones produced by the 
hypothalamus, pituitary, and ovaries. 


Estrogen 


Just prior to the middle of the cycle (approximately day 14), the high level 
of estrogen causes FSH and especially LH to rise rapidly then fall. The 
spike in LH causes the most mature follicle to rupture and release its egg. 
This is ovulation. The follicles that did not rupture degenerate and their 
eggs are lost. The level of estrogen decreases when the extra follicles 
degenerate. 


Following ovulation, the ovarian cycle enters its luteal phase and the 
menstrual cycle enters its secretory phase, both of which run from about 
day 15 to 28. The luteal and secretory phases refer to changes in the 
ruptured follicle. The cells in the follicle undergo physical changes and 
produce a structure called a corpus luteum. The corpus luteum produces 
estrogen and progesterone. The progesterone facilitates the regrowth of the 
uterine lining and inhibits the release of further FSH and LH. The uterus is 
being prepared to accept a fertilized egg, should it occur during this cycle. 
The inhibition of FSH and LH prevents any further eggs and follicles from 
developing, while the progesterone is elevated. The level of estrogen 
produced by the corpus luteum increases to a steady level for the next few 
days. 


If no fertilized egg is implanted into the uterus, the corpus luteum 
degenerates and the levels of estrogen and progesterone decrease. The 
endometrium begins to degenerate as the progesterone levels drop, 
initiating the next menstrual cycle. The decrease in progesterone also allows 
the hypothalamus to send GnRH to the anterior pituitary, releasing FSH and 
LH and starting the cycles again. 


Gestation 


Pregnancy begins with the fertilization and implantation of an egg and 
continues through to the birth of the individual. The length of time of 
gestation, or the gestation period, in humans is 266 days and is similar in 
other great apes. Gestation periods in other animals range from 12-13 days 
in the American opossum to the 660 day gestation period of the African 
elephant. 


Within 24 hours of fertilization, the egg nucleus has finished meiosis and 
the egg and sperm nuclei fuse. With fusion, the cell is known as a zygote. 
The zygote initiates cleavage and the developing embryo travels through 
the oviduct to the uterus. The developing embryo must implant into the wall 
of the uterus within seven days, or it will deteriorate and die. The outer 
layers of the developing embryo or blastocyst grow into the endometrium 
by digesting the endometrial cells, and healing of the endometrium closes 


up the blastocyst into the tissue. Another layer of the blastocyst, the 
chorion, begins releasing a hormone called human beta chorionic 
gonadotropin (B-HCG), which makes its way to the corpus luteum and 
keeps that structure active. This ensures adequate levels of progesterone 
that will maintain the endometrium of the uterus for the support of the 
developing embryo. Pregnancy tests determine the level of B-HCG in urine 
or serum. If the hormone is present, the test is positive. 


The gestation period is divided into three equal periods or trimesters. 
During the first two-to-four weeks of the first trimester, nutrition and waste 
are handled by the endometrial lining through diffusion. As the trimester 
progresses, the outer layer of the embryo begins to merge with the 
endometrium, and the placenta forms. The placenta takes over the nutrient 
and waste requirements of the embryo and fetus, with the mother’s blood 
passing nutrients to the placenta and removing waste from it. Chemicals 
from the fetus, such as bilirubin, are processed by the mother’s liver for 
elimination. Some of the mother’s immunoglobulins will pass through the 
placenta, providing passive immunity against some potential infections. 


Internal organs and body structures begin to develop during the first 
trimester. By five weeks, limb buds, eyes, the heart, and liver have been 
basically formed. By eight weeks, the term fetus applies, and the body is 
essentially formed ({link]a). The individual is about five centimeters (two 
inches) in length and many of the organs, such as the lungs and liver, are 
not yet functioning. Exposure to any toxins is especially dangerous during 
the first trimester, as all of the body’s organs and structures are going 
through initial development. Anything that interferes with chemical 
signaling during that development can have a severe effect on the fetus’ 
survival. 


(b) 


(a) Fetal development is shown at nine weeks 
gestation. (b) This fetus is just entering the second 
trimester, when the placenta takes over more of the 

functions performed as the baby develops. (c) 

There is rapid fetal growth during the third 
trimester. (credit a: modification of work by Ed 
Uthman; credit b: modification of work by 
National Museum of Health and Medicine; credit 
c: modification of work by Gray’s Anatomy) 


During the second trimester, the fetus grows to about 30 cm (about 12 
inches) ([link]b). It becomes active and the mother usually feels the first 
movements. All organs and structures continue to develop. The placenta has 
taken over the functions of nutrition and waste elimination and the 
production of estrogen and progesterone from the corpus luteum, which has 
degenerated. The placenta will continue functioning up through the delivery 
of the baby. During the third trimester, the fetus grows to 3 to 4 kg (6.5-8.5 
Ibs.) and about 50 cm (19—20 inches) long ({link]c). This is the period of the 
most rapid growth during the pregnancy as all organ systems continue to 
grow and develop. 


Labor is the name given to the muscular contractions that expel the fetus 
and placenta from the uterus. Toward the end of the third trimester, estrogen 
causes receptors on the uterine wall to develop and bind the hormone 
oxytocin. At this time, the fetus usually reorients, facing forward and down 


with the back or crown of the head pushing on the cervix (uterine opening). 
This causes the cervix to stretch and nerve impulses are sent to the 
hypothalamus, which signals the release of oxytocin from the posterior 
pituitary. Oxytocin causes smooth muscle in the uterine wall to contract. At 
the same time, the placenta releases prostaglandins into the uterus, 
increasing the contractions. A positive feedback relay occurs between the 
uterus, hypothalamus, and the posterior pituitary to assure an adequate 
supply of oxytocin. As more smooth muscle cells are recruited, the 
contractions increase in intensity and force. As noted previously, this is a 
good example of a positive feedback loop — the stimulus causes the 
production of a hormone that increases the stimulus. 


There are three stages to labor. During stage one, the cervix thins and 
dilates. This is necessary for the baby and placenta to be expelled during 
birth. The cervix will eventually dilate to about 10 cm. During stage two, 
the baby is expelled from the uterus. The uterus contracts and the mother 
pushes as she compresses her abdominal muscles to aid the delivery. The 
last stage is the passage of the placenta after the baby has been born and the 
organ has completely disengaged from the uterine wall. If labor should stop 
before stage two is reached, synthetic oxytocin, known as Pitocin, can be 
administered to restart and maintain labor. 


The Integumentary System 


Introduction 


I am not this hair, I am not this skin, I am the soul that lives within. - Jalal 
ad-Din Rumi 


Rumi's line plays on the unusual focus on hair color and skin color that 
humans have had for many centuries, and asks us to look more deeply than 
those superficial layers. That is good advice, but at the same time, those 
superficial layers of hair, skin, nails, etc. (known collectively as the 
integument) have many interesting structures, and many important 
biological functions. They protect organisms from many environmental 
hazards and injuries, including disease, as well as heat or cold. To do this, 
the integument relies on interactions with many other organ systems, 
including the circulatory, nervous, and immune systems. Its beauty is 
indeed more than skin-deep. 


The Structure of Skin 


Although you may not typically think of the skin as an organ, it is in fact 
made of tissues that work together as a single structure to perform unique 
and critical functions. The skin and its accessory structures make up the 
integumentary system, which provides the body with overall protection. 
The skin is made of multiple layers of cells and tissues, which are held to 
underlying structures by connective tissue (Figure 1). The deeper layer of 
skin is well vascularized (has numerous blood vessels). It also has 
numerous sensory, and autonomic and sympathetic nerve fibers ensuring 
communication to and from the brain. There are two main layers epidermis 
and dermis with a third connective layer the hypodermis. 

Layers of Skin 


Hair shaft 
Pore of sweat gland duct 


Epidermis 


| 
| 


Arrector pili 
muscle 


Hair follicle 


Sebaceous (oil) 
gland 


Hypodermis 
Hair root 


Hair follicle 


receptor Eccrine sweat gland 


Pacinian corpuscle 


Cutaneous vascular 
plexus 


Adipose tissue 


Sensory nerve fiber 


The skin is composed of two main layers: the epidermis, 
made of closely packed epithelial cells, and the dermis, 
made of dense, irregular connective tissue that houses 
blood vessels, hair follicles, sweat glands, and other 
structures. Beneath the dermis lies the hypodermis, 
which is composed mainly of loose connective and fatty 
tissues. 


The Epidermis 


The epidermis is composed of keratinized, stratified squamous epithelium. 
It is made of four or five layers of epithelial cells, depending on its location 
in the body. It does not have any blood vessels within it (i.e., it is 
avascular). Skin that has four layers of cells is referred to as “thin skin.” 
From deep to superficial, these layers are the stratum basale, stratum 


spinosum, stratum granulosum, and stratum corneum. Most of the skin can 
be classified as thin skin. “Thick skin” is found only on the palms of the 
hands and the soles of the feet. It has a fifth layer, called the stratum 
lucidum, located between the stratum corneum and the stratum granulosum 
({link]). 

Thin Skin versus Thick Skin 


— fee oY 
. 


- 


These slides show cross- 


sections of the epidermis and 

dermis of (a) thin and (b) 
thick skin. Note the 
significant difference in the 

thickness of the epithelial 

layer of the thick skin. From 
top, LM x 40, LM ~x 40. 

(Micrographs provided by the 
Regents of University of 


Michigan Medical School © 
2012) 


The cells in all of the layers except the stratum basale are called 
keratinocytes. A keratinocyte is a cell that manufactures and stores the 
protein keratin. Keratin is an intracellular fibrous protein that gives hair, 
nails, and skin their hardness and water-resistant properties. The 
keratinocytes in the stratum corneum are dead and regularly slough away, 
being replaced by cells from the deeper layers ({link]). 

Epidermis 


The epidermis is epithelium 
composed of multiple layers 
of cells. The basal layer 
consists of cuboidal cells, 
whereas the outer layers are 
squamous, keratinized cells, 
so the whole epithelium is 
often described as being 
keratinized stratified 
squamous epithelium. LM x 
40. (Micrograph provided by 
the Regents of University of 
Michigan Medical School © 
2012) 


Layer of the Epidermis 


Stratum basale 


The stratum basale (also called the stratum germinativum) is the deepest 
epidermal layer and attaches the epidermis to the basal lamina, below which 
lie the layers of the dermis. The cells in the stratum basale bond to the 
dermis via intertwining collagen fibers, referred to as the basement 
membrane. A finger-like projection, or fold, known as the dermal papilla 
(plural = dermal papillae) is found in the superficial portion of the dermis. 
Dermal papillae increase the strength of the connection between the 
epidermis and dermis; the greater the folding, the stronger the connections 
made ((link]).Two other cell types are found dispersed among the basal 
cells in the stratum basale. The first is a Merkel cell, which functions as a 
receptor and is responsible for stimulating sensory nerves that the brain 
perceives as touch. These cells are especially abundant on the surfaces of 
the hands and feet. The second is a melanocyte, a cell that produces the 
pigment melanin. Melanin gives hair and skin its color, and also helps 
protect the living cells of the epidermis from ultraviolet (UV) radiation 
damage. 

Layers of the Epidermis 


Dead cells filled 
with keratin 


Stratum corneum 


Stratum lucidum ——_{_ 


Lamellar granules 


— eae oun Ye S S 
Ss - aa S— 
Stratum spinosum g = = eae 6 HX Keratinocyte 
2 a 
ll < yz = 
~ 2 “SS 


if —_ Soe 
Stratum basale = Y/, 
> : Merkel cell 
Ze) 


Melanocyte 


: Sensory neuron 
Dermis 


The epidermis of thick skin has five layers: stratum 
basale, stratum spinosum, stratum granulosum, stratum 
lucidum, and stratum corneum. 


Stratum Spinosum 


As the name suggests, the stratum spinosum is spiny in appearance due to 
the protruding cell processes that join the cells via a structure called a 
desmosome. The desmosomes interlock with each other and strengthen the 
bond between the cells. It is interesting to note that the “spiny” nature of 
this layer is an artifact of the staining process. Unstained epidermis samples 
do not exhibit this characteristic appearance. The stratum spinosum is 
composed of eight to 10 layers of keratinocytes, formed as a result of cell 
division in the stratum basale ([link]). Interspersed among the keratinocytes 
of this layer is a type of dendritic cell called the Langerhans cell, which 


functions as a macrophage by engulfing bacteria, foreign particles, and 
damaged cells that occur in this layer. 


The keratinocytes in the stratum spinosum begin the synthesis of keratin 
and release a water-repelling glycolipid that helps prevent water loss from 
the body, making the skin relatively waterproof. As new keratinocytes are 
produced atop the stratum basale, the keratinocytes of the stratum spinosum 
are pushed into the stratum granulosum. 


Stratum Granulosum 


The stratum granulosum has a grainy appearance due to further changes 
to the keratinocytes as they are pushed from the stratum spinosum. The 
cells (three to five layers deep) become flatter, their cell membranes 
thicken, and they generate large amounts of the proteins keratin, which is 
fibrous, and keratohyalin, which accumulates as lamellar granules within 
the cells (see [link]). These two proteins make up the bulk of the 
keratinocyte mass in the stratum granulosum and give the layer its grainy 
appearance. The nuclei and other cell organelles disintegrate as the cells 
die, leaving behind the keratin, keratohyalin, and cell membranes that will 
form the stratum lucidum, the stratum comeum, and the accessory 
structures of hair and nails. 


Stratum Lucidum 


The stratum lucidum is a smooth, seemingly translucent layer of the 
epidermis located just above the stratum granulosum and below the stratum 
corneum. This thin layer of cells is found only in the thick skin of the 
palms, soles, and digits. The keratinocytes that compose the stratum 
lucidum are dead and flattened (see [link]). These cells are densely packed 
with eleiden, a clear protein rich in lipids, derived from keratohyalin, which 
gives these cells their transparent (i.e., lucid) appearance and provides a 
barrier to water. 


Stratum Corneum 


The stratum corneum is the most superficial layer of the epidermis and is 
the layer exposed to the outside environment (see [link]). The increased 
keratinization (also called cornification) of the cells in this layer gives it its 
name. There are usually 15 to 30 layers of cells in the stratum corneum. 
This dry, dead layer helps prevent the penetration of microbes and the 
dehydration of underlying tissues, and provides a mechanical protection 
against abrasion for the more delicate, underlying layers. Cells in this layer 
are shed periodically and are replaced by cells pushed up from the stratum 
granulosum (or stratum lucidum in the case of the palms and soles of feet). 
The entire layer is replaced during a period of about 4 weeks. Cosmetic 
procedures, such as microdermabrasion, help remove some of the dry, upper 
layer and aim to keep the skin looking “fresh” and healthy. 


Dermis 


The dermis might be considered the “core” of the integumentary system 
(derma- = “skin”), as distinct from the epidermis (epi- = “upon” or “over” 
and hypodermis (hypo- = “below”). It contains blood and lymph vessels, 
nerves, and other structures, such as hair follicles and sweat glands. The 
dermis is made of two layers of connective tissue that compose an 
interconnected mesh of elastin and collagenous fibers, produced by 
fibroblasts ({link]). 


Layers of the Dermis 


This stained slide shows the two 
components of the dermis—the 
papillary layer and the reticular 
layer. Both are made of connective 
tissue with fibers of collagen 
extending from one to the other, 
making the border between the 
two somewhat indistinct. The 
dermal papillae extending into the 
epidermis belong to the papillary 
layer, whereas the dense collagen 
fiber bundles below belong to the 
reticular layer. LM x 10. (credit: 
modification of work by 
“kilbad”/Wikimedia Commons) 


Papillary Layer 


The papillary layer is made of loose connective tissue, which means the 
collagen and elastin fibers of this layer form a loose mesh. This superficial 
layer of the dermis projects into the stratum basale of the epidermis to form 
finger-like dermal papillae (see [link]). Within the papillary layer are 
fibroblasts, a small number of fat cells (adipocytes), and an abundance of 
small blood vessels. In addition, the papillary layer contains phagocytes, 
defensive cells that help fight bacteria or other infections that have breached 
the skin. This layer also contains lymphatic capillaries, nerve fibers, and 
touch receptors called the Meissner corpuscles. 


Reticular Layer 


Underlying the papillary layer is the much thicker reticular layer, 
composed of dense, irregular connective tissue. This layer is well 
vascularized and has a rich sensory and sympathetic nerve supply. The 
reticular layer appears reticulated (net-like) due to a tight meshwork of 
fibers. Elastin fibers provide some elasticity to the skin, enabling 
movement. Collagen fibers provide structure and tensile strength, with 
strands of collagen extending into both the papillary layer and the 
hypodermis. In addition, collagen binds water to keep the skin hydrated. 
Collagen injections and Retin-A creams help restore skin turgor by either 
introducing collagen externally or stimulating blood flow and repair of the 
dermis, respectively. 


Hypodermis 


The hypodermis (also called the subcutaneous layer or superficial fascia) is 
a layer directly below the dermis and serves to connect the skin to the 
underlying fascia (fibrous tissue) of the bones and muscles. It is not strictly 
a part of the skin, although the border between the hypodermis and dermis 
can be difficult to distinguish. The hypodermis consists of well- 
vascularized, loose, areolar connective tissue and adipose tissue, which 


functions as a mode of fat storage and provides insulation and cushioning 
for the integument. 


Pigmentation 


The color of skin is influenced by a number of pigments, including melanin, 
carotene, and hemoglobin. Recall that melanin is produced by cells called 
melanocytes, which are found scattered throughout the stratum basale of the 
epidermis. The melanin is transferred into the keratinocytes via a cellular 
vesicle called a melanosome ((link]). 

Skin Pigmentation 


Surface 


Upper 
keratinocytes 


Melanosomes 


Basal 
keratinocytes 


Melanocytes 


The relative coloration of the skin depends of the amount of 
melanin produced by melanocytes in the stratum basale and 
taken up by keratinocytes. 


Melanin occurs in two primary forms. Eumelanin exists as black and 
brown, whereas pheomelanin provides a red color. Dark-skinned 
individuals produce more melanin than those with pale skin. Exposure to 
the UV rays of the sun or a tanning salon causes melanin to be 
manufactured and built up in keratinocytes, as sun exposure stimulates 
keratinocytes to secrete chemicals that stimulate melanocytes. The 
accumulation of melanin in keratinocytes results in the darkening of the 
skin, or a tan. This increased melanin accumulation protects the DNA of 
epidermal cells from UV ray damage and the breakdown of folic acid, a 
nutrient necessary for our health and well-being. In contrast, too much 
melanin can interfere with the production of vitamin D, an important 
nutrient involved in calcium absorption. Thus, the amount of melanin 
present in our skin is dependent on a balance between available sunlight 
and folic acid destruction, and protection from UV radiation and vitamin D 
production. 


It requires about 10 days after initial sun exposure for melanin synthesis to 
peak, which is why pale-skinned individuals tend to suffer sunburns of the 
epidermis initially. Dark-skinned individuals can also get sunburns, but are 
more protected than are pale-skinned individuals. Melanosomes are 
temporary structures that are eventually destroyed by fusion with 
lysosomes; this fact, along with melanin-filled keratinocytes in the stratum 
corneum sloughing off, makes tanning impermanent. 


Too much sun exposure can eventually lead to wrinkling due to the 
destruction of the cellular structure of the skin, and in severe cases, can 
cause sufficient DNA damage to result in skin cancer. When there is an 
irregular accumulation of melanocytes in the skin, freckles appear. Moles 
are larger masses of melanocytes, and although most are benign, they 
should be monitored for changes that might indicate the presence of cancer 
({link]). 

Moles 


Moles range from benign accumulations 
of melanocytes to melanomas. These 
structures populate the landscape of our 
skin. (credit: the National Cancer 
Institute) 


Accessory Structures of the Skin 
Accessory structures of the skin include hair, nails, sweat glands, and 


sebaceous glands. These structures embryologically originate from the 
epidermis and can extend down through the dermis into the hypodermis. 


Hair 


Hair is a keratinous filament growing out of the epidermis. It is primarily 
made of dead, keratinized cells. Strands of hair originate in an epidermal 
penetration of the dermis called the hair follicle. The hair shaft is the part 
of the hair not anchored to the follicle, and much of this is exposed at the 
skin’s surface. The rest of the hair, which is anchored in the follicle, lies 
below the surface of the skin and is referred to as the hair root. The hair 
root ends deep in the dermis at the hair bulb, and includes a layer of 
mitotically active basal cells called the hair matrix. The hair bulb 
surrounds the hair papilla, which is made of connective tissue and contains 
blood capillaries and nerve endings from the dermis ((Link]). 

Hair 


Medulla 
Cortex 


Cuticle 


Sebaceous 
gland 


Inner root 
sheath 


Outer root 
sheath 


Hair matrix 


Hair 
papilla 


Hair follicles originate in the 
epidermis and have many 
different parts. 


Just as the basal layer of the epidermis forms the layers of epidermis that 
get pushed to the surface as the dead skin on the surface sheds, the basal 
cells of the hair bulb divide and push cells outward in the hair root and shaft 


as the hair grows. The medulla forms the central core of the hair, which is 
surrounded by the cortex, a layer of compressed, keratinized cells that is 
covered by an outer layer of very hard, keratinized cells known as the 
cuticle. These layers are depicted in a longitudinal cross-section of the hair 
follicle ({link]), although not all hair has a medullary layer. Hair texture 
(straight, curly) is determined by the shape and structure of the cortex, and 
to the extent that it is present, the medulla. The shape and structure of these 
layers are, in turn, determined by the shape of the hair follicle. Hair growth 
begins with the production of keratinocytes by the basal cells of the hair 
bulb. As new cells are deposited at the hair bulb, the hair shaft is pushed 
through the follicle toward the surface. Keratinization is completed as the 
cells are pushed to the skin surface to form the shaft of hair that is 
externally visible. The external hair is completely dead and composed 
entirely of keratin. For this reason, our hair does not have sensation. 
Furthermore, you can cut your hair or shave without damaging the hair 
structure because the cut is superficial. Most chemical hair removers also 
act superficially; however, electrolysis and yanking both attempt to destroy 
the hair bulb so hair cannot grow. 

Hair Follicle 


The slide shows a cross-section of a hair 
follicle. Basal cells of the hair matrix in 
the center differentiate into cells of the 
inner root sheath. Basal cells at the base 

of the hair root form the outer root sheath. 


LM x 4. (credit: modification of work by 
“kilbad”/Wikimedia Commons) 


The wall of the hair follicle is made of three concentric layers of cells. The 
cells of the internal root sheath surround the root of the growing hair and 
extend just up to the hair shaft. They are derived from the basal cells of the 
hair matrix. The external root sheath, which is an extension of the 
epidermis, encloses the hair root. It is made of basal cells at the base of the 
hair root and tends to be more keratinous in the upper regions. The glassy 
membrane is a thick, clear connective tissue sheath covering the hair root, 
connecting it to the tissue of the dermis. 


Hair serves a variety of functions, including protection, sensory input, 
thermoregulation, and communication. For example, hair on the head 
protects the skull from the sun. The hair in the nose and ears, and around 
the eyes (eyelashes) defends the body by trapping and excluding dust 
particles that may contain allergens and microbes. Hair of the eyebrows 
prevents sweat and other particles from dripping into and bothering the 
eyes. Hair also has a sensory function due to sensory innervation by a hair 
root plexus surrounding the base of each hair follicle. Hair is extremely 
sensitive to air movement or other disturbances in the environment, much 
more so than the skin surface. This feature is also useful for the detection of 
the presence of insects or other potentially damaging substances on the skin 
surface. Each hair root is connected to a smooth muscle called the arrector 
pili that contracts in response to nerve signals from the sympathetic nervous 
system, making the external hair shaft “stand up.” The primary purpose for 
this is to trap a layer of air to add insulation. This is visible in humans as 
goose bumps and even more obvious in animals, such as when a frightened 
cat raises its fur. Of course, this is much more obvious in organisms with a 
heavier coat than most humans, such as dogs and cats. 


Hair Growth 


Hair grows and is eventually shed and replaced by new hair. This occurs in 
three phases. The first is the anagen phase, during which cells divide 


rapidly at the root of the hair, pushing the hair shaft up and out. The length 
of this phase is measured in years, typically from 2 to 7 years. The catagen 
phase lasts only 2 to 3 weeks, and marks a transition from the hair follicle’s 
active growth. Finally, during the telogen phase, the hair follicle is at rest 
and no new growth occurs. At the end of this phase, which lasts about 2 to 4 
months, another anagen phase begins. The basal cells in the hair matrix then 
produce a new hair follicle, which pushes the old hair out as the growth 
cycle repeats itself. Hair typically grows at the rate of 0.3 mm per day 
during the anagen phase. On average, 50 hairs are lost and replaced per day. 
Hair loss occurs if there is more hair shed than what is replaced and can 
happen due to hormonal or dietary changes. Hair loss can also result from 
the aging process, or the influence of hormones. 


Hair Color 


Similar to the skin, hair gets its color from the pigment melanin, produced 
by melanocytes in the hair papilla. Different hair color results from 
differences in the type of melanin, which is genetically determined. As a 
person ages, the melanin production decreases, and hair tends to lose its 
color and becomes gray and/or white. 


Nails 


The nail bed is a specialized structure of the epidermis that is found at the 
tips of our fingers and toes. The nail body is formed on the nail bed, and 
protects the tips of our fingers and toes as they are the farthest extremities 
and the parts of the body that experience the maximum mechanical stress 
({link]). In addition, the nail body forms a back-support for picking up 
small objects with the fingers. The nail body is composed of densely packed 
dead keratinocytes. The epidermis in this part of the body has evolved a 
specialized structure upon which nails can form. The nail body forms at the 
nail root, which has a matrix of proliferating cells from the stratum basale 
that enables the nail to grow continuously. The lateral nail fold overlaps the 
nail on the sides, helping to anchor the nail body. The nail fold that meets 
the proximal end of the nail body forms the nail cuticle, also called the 


eponychium. The nail bed is rich in blood vessels, making it appear pink, 
except at the base, where a thick layer of epithelium over the nail matrix 
forms a crescent-shaped region called the lunula (the “little moon”). The 
area beneath the free edge of the nail, furthest from the cuticle, is called the 
hyponychium. It consists of a thickened layer of stratum corneum. 


Nails 

Free edge Eponychium 
OES. Proximal nail fold Lunula 

Nail vA 2 


Nail body 
Lateral nail fold 


Lunula 
Eponychium 


Proximal nail fold 
Epidermis Dermis Phalanx Hyponychium 


The nail is an accessory structure of the integumentary 
system. 


Sweat Glands 


When the body becomes warm, sudoriferous glands produce sweat to cool 
the body. Sweat glands develop from epidermal projections into the dermis 
and are classified as merocrine glands; that is, the secretions are excreted by 
exocytosis through a duct without affecting the cells of the gland. There are 
two types of sweat glands, each secreting slightly different products. 


An eccrine sweat gland is type of gland that produces a hypotonic sweat 
for thermoregulation. These glands are found all over the skin’s surface, but 
are especially abundant on the palms of the hand, the soles of the feet, and 
the forehead ([link]). They are coiled glands lying deep in the dermis, with 
the duct rising up to a pore on the skin surface, where the sweat is released. 
This type of sweat, released by exocytosis, is hypotonic and composed 
mostly of water, with some salt, antibodies, traces of metabolic waste, and 
dermicidin, an antimicrobial peptide. Eccrine glands are a primary 


component of thermoregulation in humans and thus help to maintain 
homeostasis. 
Eccrine Gland 


Skin surface 


Eccrine sweat 
gland 


Eccrine glands are coiled glands in the 
dermis that release sweat that is 
mostly water. 


An apocrine sweat gland is usually associated with hair follicles in densely 
hairy areas, such as armpits and genital regions. Apocrine sweat glands are 
larger than eccrine sweat glands and lie deeper in the dermis, sometimes 
even reaching the hypodermis, with the duct normally emptying into the 
hair follicle. In addition to water and salts, apocrine sweat includes organic 
compounds that make the sweat thicker and subject to bacterial 
decomposition and subsequent smell. The release of this sweat is under 
both nervous and hormonal control, and plays a role in the poorly 
understood human pheromone response. Most commercial antiperspirants 
use an aluminum-based compound as their primary active ingredient to stop 
sweat. When the antiperspirant enters the sweat gland duct, the aluminum- 


based compounds precipitate due to a change in pH and form a physical 
block in the duct, which prevents sweat from coming out of the pore. 


Sebaceous Glands 


A sebaceous gland is a type of oil gland that is found all over the body and 
helps to lubricate and waterproof the skin and hair. Most sebaceous glands 
are associated with hair follicles. They generate and excrete sebum, a 
mixture of lipids, onto the skin surface, thereby naturally lubricating the dry 
and dead layer of keratinized cells of the stratum corneum, keeping it 
pliable. The fatty acids of sebum also have antibacterial properties, and 
prevent water loss from the skin in low-humidity environments. The 
secretion of sebum is stimulated by hormones, many of which do not 
become active until puberty. Thus, sebaceous glands are relatively inactive 
during childhood. 


Functions of the Skin 


The skin and accessory structures perform a variety of essential functions, 
such as protecting the body from invasion by microorganisms, chemicals, 
and other environmental factors; preventing dehydration; acting as a 
sensory organ; modulating body temperature and electrolyte balance; and 
synthesizing vitamin D. The underlying hypodermis has important roles in 
storing fats, forming a “cushion” over underlying structures, and providing 
insulation from cold temperatures. 


Protection 


The skin protects the rest of the body from the basic elements of nature 
such as wind, water, and UV sunlight. It acts as a protective barrier against 
water loss, due to the presence of layers of keratin and glycolipids in the 
stratum corneum. It also is the first line of defense against abrasive activity 
due to contact with grit, microbes, or harmful chemicals. Sweat excreted 


from sweat glands deters microbes from over-colonizing the skin surface by 
generating dermicidin, which has antibiotic properties. 


Sensory Function 


The fact that you can feel an ant crawling on your skin, allowing you to 
flick it off before it bites, is because the skin, and especially the hairs 
projecting from hair follicles in the skin, can sense changes in the 
environment. The hair root plexus surrounding the base of the hair follicle 
senses a disturbance, and then transmits the information to the central 
nervous system (brain and spinal cord), which can then respond by 
activating the skeletal muscles of your eyes to see the ant and the skeletal 
muscles of the body to act against the ant. 


The skin acts as a sense organ because the epidermis, dermis, and the 
hypodermis contain specialized sensory nerve structures that detect touch, 
surface temperature, and pain. These receptors are more concentrated on the 
tips of the fingers, which are most sensitive to touch, especially the 
Meissner corpuscle (tactile corpuscle) ([link]), which responds to light 
touch, and the Pacinian corpuscle (lamellated corpuscle), which responds 
to vibration. Merkel cells, seen scattered in the stratum basale, are also 
touch receptors. In addition to these specialized receptors, there are sensory 
nerves connected to each hair follicle, pain and temperature receptors 
scattered throughout the skin, and motor nerves innervate the arrector pili 
muscles and glands. This rich innervation helps us sense our environment 
and react accordingly. 

Light Micrograph of a Meissner Corpuscle 


In this micrograph of a skin cross-section, 
you can see a Meissner corpuscle (arrow), 
a type of touch receptor located in a 
dermal papilla adjacent to the basement 
membrane and stratum basale of the 
overlying epidermis. LM x 100. (credit: 
“Wbensmith”/Wikimedia Commons) 


Thermoregulation 


The integumentary system helps regulate body temperature through its tight 
association with the sympathetic nervous system, the division of the 
nervous system involved in our fight-or-flight responses. The sympathetic 
nervous system is continuously monitoring body temperature and initiating 
appropriate motor responses. Recall that sweat glands, accessory structures 
to the skin, secrete water, salt, and other substances to cool the body when it 
becomes warm. Even when the body does not appear to be noticeably 
sweating, approximately 500 mL of sweat (insensible perspiration) are 
secreted a day. If the body becomes excessively warm due to high 
temperatures, vigorous activity ((link]ac), or a combination of the two, 


sweat glands will be stimulated by the sympathetic nervous system to 
produce large amounts of sweat, as much as 0.7 to 1.5 L per hour for an 
active person. When the sweat evaporates from the skin surface, the body is 
cooled as body heat is dissipated. 


In addition to sweating, arterioles in the dermis dilate so that excess heat 
carried by the blood can dissipate through the skin and into the surrounding 
environment ({link]b). This accounts for the skin redness that many people 
experience when exercising. 

Thermoregulation 


Heat is retained Heat through . 
by your body radiation and convection ae 


Heat loss 


—— Skin surface 


\ Blood circulates 
___\\\.__- to surface of 
skin to dispel 
heat 


Blood circulation 
avoids surface 
-— of skin to retain yo 


(a) (b) 


During strenuous physical activities, such as skiing (a) or 
running (c), the dermal blood vessels dilate and sweat secretion 
increases (b). These mechanisms prevent the body from 
overheating. In contrast, the dermal blood vessels constrict to 
minimize heat loss in response to low temperatures (b). (credit 
a: “Trysil”/flickr; credit c: Ralph Daily) 


When body temperatures drop, the arterioles constrict to minimize heat 
loss, particularly in the ends of the digits and tip of the nose. This reduced 
circulation can result in the skin taking on a whitish hue. Although the 
temperature of the skin drops as a result, passive heat loss is prevented, and 
internal organs and structures remain warm. If the temperature of the skin 
drops too much (such as environmental temperatures below freezing), the 


conservation of body core heat can result in the skin actually freezing, a 
condition called frostbite. 


Note: 

Aging and the... 

Integumentary System 

All systems in the body accumulate subtle and some not-so-subtle changes 
as a person ages. Among these changes are reductions in cell division, 
metabolic activity, blood circulation, hormonal levels, and muscle strength 
({link]). In the skin, these changes are reflected in decreased mitosis in the 
stratum basale, leading to a thinner epidermis. The dermis, which is 
responsible for the elasticity and resilience of the skin, exhibits a reduced 
ability to regenerate, which leads to slower wound healing. The 
hypodermis, with its fat stores, loses structure due to the reduction and 


redistribution of fat, which in turn contributes to the thinning and sagging 
of skin. 


Aging 


Generally, skin, especially on the face and 
hands, starts to display the first noticeable 
signs of aging, as it loses its elasticity 
over time. (credit: Janet Ramsden) 


The accessory structures also have lowered activity, generating thinner hair 
and nails, and reduced amounts of sebum and sweat. A reduced sweating 
ability can cause some elderly to be intolerant to extreme heat. Other cells 
in the skin, such as melanocytes and dendritic cells, also become less 
active, leading to a paler skin tone and lowered immunity. Wrinkling of the 
skin occurs due to breakdown of its structure, which results from decreased 
collagen and elastin production in the dermis, weakening of muscles lying 
under the skin, and the inability of the skin to retain adequate moisture. 
Many anti-aging products can be found in stores today. In general, these 
products try to rehydrate the skin and thereby fill out the wrinkles, and 
some stimulate skin growth using hormones and growth factors. 
Additionally, invasive techniques include collagen injections to plump the 
tissue and injections of BOTOX® (the name brand of the botulinum 
neurotoxin) that paralyze the muscles that crease the skin and cause 
wrinkling. 


Vitamin D Synthesis 


The epidermal layer of human skin synthesizes vitamin D when exposed to 
UV radiation. In the presence of sunlight, a form of vitamin D3 called 
cholecalciferol is synthesized from a derivative of the steroid cholesterol in 
the skin. The liver converts cholecalciferol to calcidiol, which is then 
converted to calcitriol (the active chemical form of the vitamin) in the 
kidneys. Vitamin D is essential for normal absorption of calcium and 
phosphorous, which are required for healthy bones. The absence of sun 
exposure can lead to a lack of vitamin D in the body, leading to a condition 
called rickets, a painful condition in children where the bones are 
misshapen due to a lack of calcium, causing bowleggedness. Elderly 
individuals who suffer from vitamin D deficiency can develop a condition 
called osteomalacia, a softening of the bones. In present day society, 
vitamin D is added as a supplement to many foods, including milk and 
orange juice, compensating for the need for sun exposure. 


In addition to its essential role in bone health, vitamin D is essential for 
general immunity against bacterial, viral, and fungal infections. Recent 


studies are also finding a link between insufficient vitamin D and cancer. 


Sensory Systems 


Introduction 

" The act of smelling something, anything, is remarkably like the act of 
thinking. Immediately at the moment of perception, you can feel the mind 
going to work, sending the odor around from place to place, setting off 
complex repertories through the brain, polling one center after another for 
signs of recognition, for old memories and old connection." Lewis Thomas, 
On Smell, 1985 


Senses provide information about the body and its environment. Humans 
have five special senses: olfaction (smell), gustation (taste), equilibrium 
(balance and body position), vision, and hearing. Additionally, we possess 
general senses, also called somatosensation, which respond to stimuli like 
temperature, pain, pressure, and vibration. Vestibular sensation, which is an 
organism’s sense of spatial orientation and balance, proprioception (position 
of bones, joints, and muscles), and the sense of limb position that is used to 
track kinesthesia (limb movement) are part of somatosensation. Although 
the sensory systems associated with these senses are very different, all share 
a common function: to convert a stimulus (such as light, or sound, or the 
position of the body) into an electrical signal in the nervous system. This 
process is called sensory transduction. We are going to focus on the five 
special senses of humans. 


There are three types of stimuli that are detected by the human sensory 
systems. The first is chemical stimulus, where molecules stimulate a 
sensory neuron. Chemical stimuli are detected by the olfactory system, 
when molecules in the air bind to sensory cells in the nasal epithelia, and in 
the gustation (taste) system, when molecules in your food stimulate your 
taste buds. The second is electromagnetic radiation; light interacts with 
molecules in the sensory cells (rods and cones) of your retina, and those 
sensory cells send a signal to your brain. The third is mechanical 
stimulation, where the sensory cells are activated by movement or touch. 
Mechanical stimuli are detected by the cells in the inner ear that help you 
detect balance and body position, and by other cells in your inner ear detect 
sound (the sense of hearing). Additionally, mechanical stimuli are involved 
in other somatosensory systems, such as pressure, pain, or vibration, in 


proprioception (position of legs, arms and other body parts), and in 
kinesthesia (detection of motion of those same body parts. 


Sensory Perception 


Reception 


The first step in sensation is reception, which is the activation of sensory 
receptors by stimuli such as mechanical stimuli (being bent or squished, for 
example), chemicals, or temperature. The receptor can then respond to the 
stimuli. The region in space in which a given sensory receptor can respond 
to a stimulus, be it far away or in contact with the body, is that receptor’s 
receptive field. Think for a moment about the differences in receptive fields 
for the different senses. For the sense of touch, a stimulus must come into 
contact with body. For the sense of hearing, a stimulus can be a moderate 
distance away (some baleen whale sounds can propagate for many 
kilometers). For vision, a stimulus can be very far away; for example, the 
visual system perceives light from stars at enormous distances. 


Transduction 


The most fundamental function of a sensory system is the translation of a 
sensory signal to an electrical signal in the nervous system. This takes place 
at the sensory receptor, and a produces a change in electrical potential in 
response to the stimulus. This is called the receptor potential. How is 
sensory input, such as pressure on the skin, changed to a receptor potential? 
In one example, a type of receptor called a mechanoreceptor (as shown in 
[link]) possesses specialized membranes that respond to pressure. 
Disturbance of these dendrites by compressing them or bending them opens 
gated ion channels in the plasma membrane of the sensory neuron, 
changing its electrical potential. Recall that in the nervous system, a 
positive change of a neuron’s electrical potential (also called the membrane 
potential), depolarizes the neuron. Receptor potentials are graded potentials: 
the magnitude of these graded (receptor) potentials varies with the strength 
of the stimulus. If the magnitude of depolarization is sufficient (that is, if 


membrane potential reaches a threshold), the neuron will fire an action 
potential. In all cases the appropriate stimulus will cause a change in the 
membrane potential of the sensory cell; the exact mechanism for changing 
the membrane potential will be different for different sensory calls. 


Tectorial membrane 


Plasma 
membrane 


> Outer hair cells 


Tectorial membrane 


Stereocillia 
Deflected 


aaa ae UU | 


Cytoskeleton 


Basilar membrane Cochlear nerve Inner hair cell 


(a) (b) 


(a) Mechanosensitive ion channels are gated ion channels that 
respond to mechanical deformation of the plasma membrane. A 
mechanosensitive channel is connected to the plasma 
membrane and the cytoskeleton by hair-like tethers. When 
pressure causes the extracellular matrix to move, the channel 
opens, allowing ions to enter or exit the cell. (b) Stereocilia in 
the human ear are connected to mechanosensitive ion channels. 
When a sound causes the stereocilia to move, 


mechanosensitive ion channels transduce the signal to the 
cochlear nerve. 


Sensory receptors for different senses are very different from each other, 
and they are specialized according to the type of stimulus they sense: they 
have receptor specificity. For example, touch receptors, light receptors, and 
sound receptors are each activated by different stimuli. Touch receptors are 
not sensitive to light or sound; they are sensitive only to touch or pressure. 
However, stimuli may be combined at higher levels in the brain, as happens 
with olfaction, contributing to our sense of taste. 


Perception 


Perception is an individual’s interpretation of a sensation. Although 
perception relies on the activation of sensory receptors, perception happens 
not at the level of the sensory receptor, but at higher levels in the nervous 
system, in the brain. The brain distinguishes sensory stimuli through a 
sensory pathway: action potentials from sensory receptors travel along 
neurons that are dedicated to a particular stimulus. These neurons are 
dedicated to that particular stimulus and synapse with particular neurons in 
the brain or spinal cord. 


All sensory signals, except those from the olfactory system, are transmitted 
though the central nervous system and are routed to the thalamus and to the 
appropriate region of the cortex. Recall that the thalamus is a structure in 
the forebrain that serves as a clearinghouse and relay station for sensory (as 
well as motor) signals. When the sensory signal exits the thalamus, it is 
conducted to the specific area of the cortex ([link]) dedicated to processing 
that particular sense. 


How are neural signals interpreted? Interpretation of sensory signals 
between individuals of the same species is largely similar, owing to the 
inherited similarity of their nervous systems; however, there are some 
individual differences. A good example of this is individual tolerances to a 


painful stimulus, such as dental pain, which certainly differ. Interestingly, 
studies have shown that the allele that results in red hair in humans 
homozygous for that allele (known as MC1R) is a member of the family of 
sensory receptors that detect pain. And redheads are more sensitive to pain, 
and require about 20% more anesthetic during surgery or dental work. So 
be nice to your red-headed friends. 


Somatosensory 
“processing region 


Auditory processing Visual processing 
region region 


(a) (b) 


In humans, with the exception of olfaction, all sensory 
signals are routed from the (a) thalamus to (b) final 
processing regions in the cortex of the brain. (credit b: 
modification of work by Polina Tishina) 


Taste and Smell 


Taste, also called gustation, and smell, also called olfaction, are the most 
interconnected senses in that both involve molecules of the stimulus 
entering the body and bonding to receptors. Smell lets an animal sense the 
presence of food or other animals—whether potential mates, predators, or 
prey—or other chemicals in the environment that can impact their survival. 
Similarly, the sense of taste allows animals to discriminate between types of 
foods. While the value of a sense of smell is obvious, what is the value of a 
sense of taste? Different tasting foods have different attributes, both helpful 


and harmful. For example, sweet-tasting substances tend to be highly 
caloric, which could be necessary for survival in lean times. Bitterness is 
associated with toxicity, and sourness is associated with spoiled food. Salty 
foods are valuable in maintaining homeostasis by helping the body retain 
water and by providing ions necessary for cells to function. 


Tastes and Odors 


Both taste and odor stimuli are molecules taken in from the environment. 
The primary tastes detected by humans are sweet, sour, bitter, salty and 
umami. The first four tastes need little explanation. The identification of 
umami as a fundamental taste occurred fairly recently—it was identified in 
1908 by Japanese scientist Kikunae Ikeda while he worked with seaweed 
broth, but it was not widely accepted as a taste that could be physiologically 
distinguished until many years later. The taste of umami, also known as 
savoriness, is attributable to the taste of the amino acid L-glutamate. In fact, 
monosodium glutamate, or MSG, is often used in cooking to enhance the 
savory taste of certain foods. What is the adaptive value of being able to 
distinguish umami? Savory substances tend to be high in protein. 


All odors that we perceive are volatile chemicals in the air we breathe. If a 
substance does not release molecules into the air from its surface, it has no 
smell. And if a human or other animal does not have a receptor that 
recognizes a specific molecule, then that molecule has no smell. Humans 
have about 350 olfactory receptor subtypes that work in various 
combinations to allow us to sense about 10,000 different odors. Compare 
that to mice, for example, which have about 1,300 olfactory receptor types, 
and therefore probably sense more odors. Both odors and tastes involve 
molecules that stimulate specific chemoreceptors. Although humans 
commonly distinguish taste as one sense and smell as another, they work 
together to create the perception of flavor. A person’s perception of flavor is 
reduced if he or she has congested nasal passages. 


Reception and Transduction 


Taste 


Detecting a taste (gustation) is fairly similar to detecting an odor 
(olfaction), given that both taste and smell rely on chemical receptors being 
stimulated by certain molecules. The primary organ of taste is the taste bud. 
A taste bud is a cluster of gustatory receptors (taste cells) that are located 
within the bumps on the tongue called papillae (singular: papilla) 
(illustrated in [link]). 


Circumvallate papillae 
Foliate 


papillae Fungiform papillae 


Filiform papillae 


(a) Foliate, circumvallate, and fungiform papillae are 
located on different regions of the tongue. (b) Foliate 
papillae are prominent protrusions on this light micrograph. 
(credit a: modification of work by NCI; scale-bar data from 
Matt Russell) 


Each taste bud’s taste cells are replaced every 10 to 14 days. These are 
elongated cells with hair-like processes called microvilli at the tips that 
extend into the taste bud pore (illustrate in [link]). Food molecules (tastants) 
are dissolved in saliva, and they bind with and stimulate the receptors on 
the microvilli. The receptors for tastants are located across the outer portion 
and front of the tongue, outside of the middle area where the filiform 
papillae are most prominent. 


Oral Cavity Microvilli Taste pore 


ee 
“> Epidermis of tongue 


\- Supporting 
mm cell 


yp 


Pores in the tongue allow tastants to enter taste 
pores in the tongue. (credit: modification of 
work by Vincenzo Rizzo) 


In humans, there are five primary tastes, and each taste has only one 
corresponding type of receptor. Thus, like olfaction, each receptor is 
specific to its stimulus (tastant). Both tasting abilities and sense of smell 
change with age. In humans, the senses decline dramatically by age 50 and 
continue to decline. A child may find a food to be too spicy, whereas an 
elderly person may find the same food to be bland and unappetizing. 


Hearing and Equilibrium 


Audition, or hearing, is important to humans and to other animals for many 
different interactions. It enables an organism to detect and receive 
information about danger, such as an approaching predator, and to 
participate in communal exchanges like those concerning territories or 
mating. On the other hand, although it is physically linked to the auditory 
system, the vestibular system is not involved in hearing. Instead, an 


animal’s vestibular system detects its own movement, both linear and 
angular acceleration and deceleration, and balance. 


Sound 


Auditory stimuli are sound waves, which are mechanical, pressure waves 
that move through a medium, such as air or water. There are no sound 
waves in a vacuum since there are no air molecules to move in waves. The 
speed of sound waves differs, based on altitude, temperature, and medium, 
but at sea level and a temperature of 20° C (68° F), sound waves travel in 
the air at about 343 meters per second. 


As is true for all waves, there are four main characteristics of a sound wave: 
frequency, wavelength, period, and amplitude. Frequency is the number of 
waves per unit of time, and in sound is heard as pitch. High-frequency 
(>15.000Hz) sounds are higher-pitched (short wavelength) than low- 
frequency (long wavelengths; <100Hz) sounds. Frequency is measured in 
cycles per second, and for sound, the most commonly used unit is hertz 
(Hz), or cycles per second. Most humans can perceive sounds with 
frequencies between 30 and 20,000 Hz. Women are typically better at 
hearing high frequencies, but everyone’s ability to hear high frequencies 
decreases with age. Dogs detect up to about 40,000 Hz; cats, 60,000 Hz; 
bats, 100,000 Hz; and dolphins 150,000 Hz, and American shad (Alosa 
sapidissima), a fish, can hear 180,000 Hz. Those frequencies above the 
human range are called ultrasound. 


Reception of Sound 


In mammals, sound waves are collected by the external, cartilaginous part 
of the ear called the pinna, then travel through the auditory canal and cause 
vibration of the thin diaphragm called the tympanum or ear drum, the 
innermost part of the outer ear (illustrated in [link]). Interior to the 
tympanum is the middle ear. The middle ear holds three small bones called 
the ossicles, which transfer energy from the moving tympanum to the inner 


ear. The three ossicles are the malleus (also known as the hammer), the 
incus (the anvil), and stapes (the stirrup). The aptly named stapes looks very 
much like a stirrup. The three ossicles are unique to mammals, and each 
plays a role in hearing. The malleus attaches at three points to the interior 
surface of the tympanic membrane. The incus attaches the malleus to the 
stapes. In humans, the stapes is not long enough to reach the tympanum. If 
we did not have the malleus and the incus, then the vibrations of the 
tympanum would never reach the inner ear. These bones also function to 
collect force and amplify sounds. The ear ossicles are homologous to bones 
in a fish mouth: the bones that support gills in fish are thought to have been 
adapted for use in the vertebrate ear over evolutionary time. 


Stapes 
(attached to oval window) 


Semicircular 


Malleus 
Vestibular nerve 


Cochlear 
nerve 


Cochlea 


Ear canal ; 
Tympanic 
cavity 


Tympanum Eustachian tube 


Round window 


Sound travels through the outer ear to the middle ear, which 
is bounded on its exterior by the tympanic membrane. The 
middle ear contains three bones called ossicles that transfer 
the sound wave to the oval window, the exterior boundary 
of the inner ear. The organ of Corti, which is the organ of 
sound transduction, lies inside the cochlea. (credit: 
modification of work by Lars Chittka, Axel Brockmann) 


Vestibular Information 


The stimuli associated with the vestibular system are linear acceleration 
(gravity) and angular acceleration and deceleration. Gravity, acceleration, 
and deceleration are detected by evaluating the inertia on receptive cells in 
the vestibular system. Gravity is detected through head position. Angular 
acceleration and deceleration are expressed through turning or tilting of the 
head. 


The vestibular system has some similarities with the auditory system. It 
utilizes hair cells just like the auditory system, but it excites them in 
different ways. There are five vestibular receptor organs in the inner ear: the 
utricle, the saccule, and three semicircular canals. Together, they make up 
what’s known as the vestibular labyrinth that is shown in [link]. The utricle 
and saccule respond to acceleration in a straight line, such as gravity. The 
roughly 30,000 hair cells in the utricle and 16,000 hair cells in the saccule 
lie below a gelatinous layer, with their stereocilia projecting into the gelatin. 
Embedded in this gelatin are calcium carbonate crystals—like tiny rocks. 
When the head is tilted, the crystals continue to be pulled straight down by 
gravity, but the new angle of the head causes the gelatin to shift, thereby 
bending the stereocilia. The bending of the stereocilia stimulates the 
neurons, and they signal to the brain that the head is tilted, allowing the 
maintenance of balance. It is the vestibular branch of the vestibulocochlear 
cranial nerve that deals with balance. 


Posterior Canal 
Superior Canal 


Urticle 


=o 

a , Cochlea 
vy 
es, \ 


Horizontal 
Canal 


Vestibule 


Saccule 


The structure of the vestibular 
labyrinth is shown. (credit: 
modification of work by NIH) 


The fluid-filled semicircular canals are tubular loops set at oblique angles. 
They are arranged in three spatial planes. The base of each canal has a 
swelling that contains a cluster of hair cells. The hairs project into a 
gelatinous cap called the cupula and monitor angular acceleration and 
deceleration from rotation. They would be stimulated by driving your car 
around a corner, turning your head, or falling forward. One canal lies 
horizontally, while the other two lie at about 45 degree angles to the 
horizontal axis, as illustrated in [link]. When the brain processes input from 
all three canals together, it can detect angular acceleration or deceleration in 
three dimensions. When the head turns, the fluid in the canals shifts, 
thereby bending stereocilia and sending signals to the brain. Upon cessation 
accelerating or decelerating—or just moving—the movement of the fluid 
within the canals slows or stops. For example, imagine holding a glass of 
water. When moving forward, water may splash backwards onto the hand, 
and when motion has stopped, water may splash forward onto the fingers. 
While in motion, the water settles in the glass and does not splash. Note that 
the canals are not sensitive to velocity itself, but to changes in velocity, so 
moving forward at 6(0mph with your eyes closed would not give the 
sensation of movement, but suddenly accelerating or braking would 


stimulate the receptors. 


Vision 


Vision is the ability to detect light patterns from the outside environment 
and interpret them into images. Animals are bombarded with sensory 
information, and the sheer volume of visual information can be 
problematic. Fortunately, the visual systems of species have evolved to 
attend to the most-important stimuli. The importance of vision to humans is 
further substantiated by the fact that about one-third of the human cerebral 
cortex is dedicated to analyzing and perceiving visual information. 


Light 


As with auditory stimuli, light travels in waves. The compression waves 
that compose sound must travel in a medium—a gas, a liquid, or a solid. In 
contrast, light is composed of electromagnetic waves and needs no medium; 
light can travel in a vacuum ((link]). The behavior of light can be discussed 
in terms of the behavior of waves and also in terms of the behavior of the 
fundamental unit of light—a packet of electromagnetic radiation called a 
photon. A glance at the electromagnetic spectrum shows that visible light 
for humans is just a small slice of the entire spectrum, which includes 
radiation that we cannot see as light because it is below the frequency of 
visible red light and above the frequency of visible violet light. 


Certain variables are important when discussing perception of light. 
Wavelength (which varies inversely with frequency) manifests itself as hue. 
Light at the red end of the visible spectrum has longer wavelengths (and is 
lower frequency), while light at the violet end has shorter wavelengths (and 
is higher frequency). The wavelength of light is expressed in nanometers 
(nm); one nanometer is one billionth of a meter. Humans perceive light that 
ranges between approximately 380 nm and 740 nm. Some other animals, 
though, can detect wavelengths outside of the human range. For example, 
bees see near-ultraviolet light in order to locate nectar guides on flowers, 
and some non-avian reptiles sense infrared light (heat that prey gives off). 


Wavelength 


(meters) Radio Microwave Infrared Visible Ultraviolet X-ray Gamma ray 


10° 10? 10° 5x 10° 10° 107° 10 


line a x ee @ 


Buildings Humans Honeybee Pinpoint Protozoans Molecules Atoms Atomic nuclei 
I SSS 
(Hz) 
10* 108 10% 10% 10** 108 10” 


In the electromagnetic spectrum, visible light lies between 
380 nm and 740 nm. (credit: modification of work by 
NASA) 


Wave amplitude is perceived as luminous intensity, or brightness. The 
standard unit of intensity of light is the candela, which is approximately the 
luminous intensity of a one common candle. 


Light waves travel 299,792 km per second in a vacuum, (and somewhat 
slower in various media such as air and water), and those waves atrive at 
the eye as long (red), medium (green), and short (blue) waves. What is 
termed “white light” is light that is perceived as white by the human eye. 
This effect is produced by light that stimulates equally the color receptors in 
the human eye. The apparent color of an object is the color (or colors) that 
the object reflects. Thus a red object reflects the red wavelengths in mixed 
(white) light and absorbs all other wavelengths of light. 


Anatomy of the Eye 


The photoreceptive cells of the eye, where transduction of light to nervous 
impulses occurs, are located in the retina (shown in [link]) on the inner 
surface of the back of the eye. But light does not impinge on the retina 
unaltered. It passes through other layers that process it so that it can be 


interpreted by the retina ([link]b). The cornea, the front transparent layer of 
the eye, and the crystalline lens, a transparent convex structure behind the 
comea, both refract (bend) light to focus the image on the retina. The iris, 
which is conspicuous as the colored part of the eye, is a circular muscular 
ring lying between the lens and cornea that regulates the amount of light 
entering the eye. In conditions of high ambient light, the iris contracts, 
reducing the size of the pupil at its center. In conditions of low light, the iris 
relaxes and the pupil enlarges. 


Optic nerve 


Light 
Cornea 
._— Aqueous humour wy > wy > ~s 


Retina 
Ganglion 
cells 


Vitreous / 
humour bs Amacrine 
y cells 


Bipolar cells 


Horizontal 
cells 


Optic nerve 


Fovea | =— Cone 


Retinal 
blood vessels 


(a) The human eye is shown in cross section. (b) A blowup 
shows the layers of the retina. 


The main function of the lens is to focus light on the retina and fovea 
centralis. The lens is dynamic, focusing and re-focusing light as the eye 
rests on near and far objects in the visual field. The lens is operated by 
muscles that stretch it flat or allow it to thicken, changing the focal length 
of light coming through it to focus it sharply on the retina. With age comes 
the loss of the flexibility of the lens, and a form of farsightedness called 
presbyopia results. Presbyopia occurs because the image focuses behind the 
retina. Presbyopia is a deficit similar to a different type of farsightedness 


called hyperopia caused by an eyeball that is too short. For both defects, 
images in the distance are clear but images nearby are blurry. Myopia 
(nearsightedness) occurs when an eyeball is elongated and the image focus 
falls in front of the retina. In this case, images in the distance are blurry but 
images nearby are clear. 


There are two types of photoreceptors in the retina: rods and cones, named 
for their general appearance as illustrated in [link]. Rods are strongly 
photosensitive and are located in the outer edges of the retina. They detect 
dim light and are used primarily for peripheral and nighttime vision. Cones 
are weakly photosensitive and are located near the center of the retina. They 
respond to bright light, and their primary role is in daytime, color vision. 


Outer segment 
contains rhodopsin 


Rod outer 
segment 


Outer segment 
contains 
photopigments 


Oil droplet 
Nucleus 


Rods and cones are photoreceptors 
in the retina. Rods respond in low 
light and can detect only shades of 
gray. Cones respond in intense 
light and are responsible for color 
vision. (credit: modification of 
work by Piotr Sliwa) 


The fovea is the region in the center back of the eye that is responsible for 
acute vision. The fovea has a high density of cones. When you bring your 
gaze to an object to examine it intently in bright light, the eyes orient so that 
the object’s image falls on the fovea. However, when looking at a star in the 
night sky or other object in dim light, the object can be better viewed by the 
peripheral vision because it is the rods at the edges of the retina, rather than 
the cones at the center, that operate better in low light. In humans, cones far 
outnumber rods in the fovea. 


Transduction of Light 


The rods and cones are the site of transduction of light to a neural signal. 
Both rods and cones contain photopigments. In vertebrates, the main 
photopigment, rhodopsin, has two main parts: an opsin, which is a 
membrane protein (in the form of a cluster of a-helices that span the 
membrane), and retinal—a molecule that absorbs light. When light hits a 
photoreceptor, it causes a shape change in the retinal, altering its structure 
from a bent (cis) form of the molecule to its linear (trans) isomer. This 
isomerization of retinal activates the rhodopsin, starting a cascade of events 
that ends with a change in the membrane potential of the rod or cone cell. 


Trichromatic Coding 


There are three types of cones (with different photopsins), and they differ in 
the wavelength to which they are most responsive, as shown in [link]. Some 
cones are maximally responsive to short light waves of 420 nm, so they are 
called S cones (“S” for “short”); others respond maximally to waves of 530 
nm (M cones, for “medium”); a third group responds maximally to light of 
longer wavelengths, at 560 nm (L, or “long” cones). With only one type of 
cone, color vision would not be possible, and a two-cone (dichromatic) 
system has limitations. Primates use a three-cone (trichromatic) system, 
resulting in full color vision. 


The color we perceive is a result of the ratio of activity of our three types of 
cones. The colors of the visual spectrum, running from long-wavelength 


light to short, are red (700 nm), orange (600 nm), yellow (565 nm), green 
(497 nm), blue (470 nm), indigo (450 nm), and violet (425 nm). Humans 
have very sensitive perception of color and can distinguish about 500 levels 
of brightness, 200 different hues, and 20 steps of saturation, or about 2 
million distinct colors. 


Normalized absorbance 


400 500 600 700 


Wavelength (nm) 


Human rod cells and the different types of 
cone cells each have an optimal 
wavelength. However, there is 

considerable overlap in the wavelengths 
of light detected. 


Reflexes and Homeostasis 


Introduction 

"There is no other species on Earth that does science. It is, so far, entirely a 
human invention, evolved by natural selection in the human cortex for one 
simple reason: it works. It is not perfect. It is misused. It is only a tool. But 
it is by far the best tool we have, self-correcting, ongoing, applicable to 
everything.” Carl Sagan, American astronomer, in Cosmos, 1980 


As we come to the last section of this book, it seems appropriate to hearken 
back to where we started - with a reminder that science is a way of 
knowing. The knowledge of animal biology discussed in this module, and 
the mechanisms of nervous system function, homeostasis, etc. are all 
products of painstaking experiments and observations, in some cases dating 
back hundreds of years. This uniquely human endeavor gave us that 
knowledge. More importantly, animal biology is just a subset of the science 
of biology, and biology is just a subset of science. There is a lot more to 
explore in other areas of science, and infinitely more for current and future 
humans to learn about all of them. We hope that the knowledge and 
thinking processes that you have used in this course will serve you well in 
your future education, and will help you attain success in whatever 
endeavor you choose for your future work. 


Reflexes 


When the body reacts involuntarily to an internal or external stimulus, the 
response is called a reflex, and the neurons that make up the simple circuit 
are called a reflex arc. This is involuntary, spontaneous, and does not 
involve processing of stimuli by higher centers (e.g. regions of the brain). 
Reflexes can be spinal or cranial, depending on the nerves and central 
components that are involved. For example heat and pain sensations from a 
hot stove causing withdrawal of the arm through a connection in the spinal 
cord that leads to contraction of the muscles in the arm, jerking the arm 
away from the hot stove. 


Other examples of reflexes include 


¢ Withdrawal reflex, which occurs when you step on a painful 
stimulus, like a tack or a sharp rock. The pain receptors (nociceptors) 
that are activated by the painful stimulus activate the motor neurons 
responsible for contraction of the leg muscles to remove your foot 
from the pain. 

¢ Stretch reflex, which helps to maintain muscles and an optimal length. 
Receptors (called spindle receptors) within muscles are activated when 
the muscle is stretched, causing direct contraction of the muscle. 

¢ Corneal reflex, or eye-blink reflex. When the cornea is stimulated, 
whether by touch or a bright light, blinking of the eyelids is initiated. 
Obviously this is to keep the cornea safe from abrasion by dust or 
flying insects, etc, and to protect the lens and retina from over-bright 
light. There are more nerves per square inch in your cornea than in any 
other part of your body! 


The autonomic nervous system regulates organ systems through circuits 
that resemble the reflexes of the somatic nervous system such as the knee 
jerk reflex. The main difference between the somatic and autonomic 
systems is in what target tissues are effectors. Somatic responses are solely 
based on skeletal muscle contraction. The autonomic system, however, 
targets cardiac and smooth muscle, as well as glandular tissue. Whereas the 
basic circuit is a reflex arc, there are differences in the structure of those 
reflexes for the somatic and autonomic systems. 


Components of the Reflex Arc 


There are typically three neurons in a reflex arc. These are a sensory 
neuron, which responds to a sensory stimulus (touch, pain, muscle stretch, 
etc.); an interneuron, which receives a signal if the sensory neuron is 
stimulated sufficiently; and a motor neuron, which is stimulated by the 
interneuron and then carries out the action required for the stimulus which 
initiated the response. The sensory neurons can be oriented externally (i.e., 
to detect stimuli coming from outside the body), in internally, to detect 
stimuli originating in the body. An example of the latter would be the 
stretch receptors that tell your stomach to start contracting harder after a big 
meal, or the pressure receptors (baroreceptors) in your carotid arteries 
which detect blood pressure and tell your heart to beat faster or slower, 


according to the pressure that they are sensing. Similarly, the interneurons 
fall into two general categories. In long reflexes, the interneuron is in a 
central nervous system (CNS) structure such as the brain or spinal cord. In 
short reflexes, the interneuron is located in a peripheral ganglion, bypassing 
the CNS, as shown in [link]. Finally, the motor neurons which generates the 
response can also be classified into two general categories. One type of 
motor neuron innervates a muscle, and stimulates contraction of that 
muscle, and the subsequent rapid removal of your hand from a hot stove, or 
a more rapid heartbeat, for example. The second class innervates a gland, 
and causes secretion of hormones that mediate the appropriate response. An 
example of the latter would be the nerves which cause the adrenal gland to 
release adrenaline as part of the fight-or-flight response when you see a lion 
or tiger or bear coming at you. 


Short and Long Reflexes 


Short and Long Reflexes 


Long Reflex 


Sensory receptor cell 
— 
Sensory cell synapses os =i 
in spinal cord or brain SES 
} Z, 


Short Reflex 


Sensory receptor cell 
oF =-5- pe (« Sensation 


Sensory cell synapses only 
in peripheral ganglion 


Sensory input can stimulate either a short or a long reflex. 
A sensory neuron can project to the CNS or to an 
autonomic ganglion. The short reflex involves the direct 
stimulation of a postganglionic fiber by the sensory neuron, 
whereas the long reflex involves integration in the spinal 
cord or brain. 


Homeostasis 


As we come to the end of this module, it is appropriate to revisit the 
concept of homeostasis as a unifying theme in biology. The reflexes 
described above are just one example homeostatic mechanisms that allow 


organisms to maintain the parameters of their internal environment about an 
optimal setting. The organ systems described in this section also all have 
many examples of homeostatic mechanisms that allow those organ systems 
to maintain optimal levels of other parameters, such as oxygen levels in the 
blood, or the pH of the contents of the duodenum. All of these organ 
systems work together for the benefit, survival and reproduction of the 
organism. The organ systems are highly interconnected as well. The 
circulatory and respiratory systems must coordinate their functions, since 
the function of one is to circulate the needed gases and waste products that 
come in and go out via the other system. The osmoregulatory system also 
has to work hand-in-hand with the circulatory and respiratory system to 
maintain the content of the blood at optimal levels, the digestive system has 
to provide the nutrients for all of these other organs to function, the nervous 
and endocrine systems have to respond to a variety of external and internal 
signals, etc. Finally, the organisms that compose populations and 
communities and ecosystems also seem to interact with the abiotic 
components (e.g. nutrients) of the ecosystem in a homeostatic fashion; for 
example, the CO, needed by plants is emitted by other organisms, and the 
level of atmospheric CO, has remained relatively constant over many 
millenia. 


But it is becoming ever more clear that the activities of one species on the 
planet, Homo sapiens, is resetting the set points for these homeostatic 
processes. As we currently burn about a million years worth of past net 
primary productivity every year, we are seeing the atmospheric CO) levels 
slowly rise, as you learned in an earlier module. The effects of changing the 
amount of that globally important compound, over a short time span, 
geologically speaking, are just starting to be realized. But it is clear that 
there will be many ramifications, even if we don't yet understand all of 
them. It is hoped that your newfound understanding of biological 
interactions and homeostatic mechanisms will enable your generation to 
devise appropriate strategies that will again demonstrate that the "sapiens" 
part of our name is a good descriptor for our species. It will take both the 
knowledge you have gained in this class, and the wisdom you will gain in 
all your classes and experiences, to meet the challenges ahead. 


Viruses 


Introduction 

"That's the salubrious thing about zoonotic diseases: they remind us, as 
Saint Francis did, that we humans are inseparable from the natural world. In 
fact, there is no "natural world", its a bad and artificial phrase. There is only 
the world. Humankind is part of that world, as are the ebola viruses, as are 
the influenzas and the HIVs, as are Marburg and Nipah and SARS, as are 
chimpanzees and palm civets and Egyptian fruit bats, as is the next 
murderous virus - the one we haven't yet discovered." David Quammen, 


(a) The tobacco mosaic virus, seen by transmission 
electron microscopy, was the first virus to be 
discovered. (b) The leaves of an infected plant are 
shown. (credit a: scale-bar data from Matt Russell; 
credit b: modification of work by USDA, Department 
of Plant Pathology Archive, North Carolina State 
University) 


No one knows exactly when viruses emerged or from where they came, 
since viruses do not leave physical evidence in the form of fossils. Modern 
viruses are thought to be a mosaic of bits and pieces of nucleic acids picked 
up from various sources along their respective evolutionary paths. Viruses 
are acellular, parasitic entities that are not classified within any of the three 
domains because they are not exactly alive. But they do parasitize, evolve, 
reproduce and co-evolve with other organisms; they inhabit a shadowy 
world that may not be alive, but is very close to it. They have no plasma 


membrane, internal organelles, or metabolic processes, and they do not 
divide. Instead, they infect a host cell and use the host’s replication 
processes to produce progeny virus particles. Viruses infect all forms of 
organisms including bacteria, archaea, fungi, plants, and animals. 


Viruses are diverse. They vary in their structure, their replication methods, 
and in their target hosts or even host cells. They infect every type of 
organism known, from Archaea to Bacteria to Eukaryotes, and are found in 
every environment. They are also remarkably abundant; it is estimated that 
each milliliter of sea water contains 10” viruses, both DNA and RNA 
varieties. They are major players in the evolution of the life forms on this 
planet; genes derived from viruses allowed mammals to develop a placenta, 
for example. 


How Viruses Replicate 


Viruses were first discovered after the development of a porcelain filter, 
called the Chamberland-Pasteur filter, which could remove all bacteria 
visible under the microscope from any liquid sample. In 1886, Adolph 
Meyer demonstrated that a disease of tobacco plants, tobacco mosaic 
disease, could be transferred from a diseased plant to a healthy one through 
liquid plant extracts. In 1892, Dmitri Ivanowski showed that this disease 
could be transmitted in this way even after the Chamberland-Pasteur filter 
had removed all viable bacteria from the extract. Still, it was many years 
before it was proven that these “filterable” infectious agents were not 
simply very small bacteria but were a new type of tiny, disease-causing 
particle. 


Virions, single virus particles, are very small, about 20—250 nanometers (1 
nanometer = 1/1,000,000 mm); although the recent discovery of entities 
called Pandoraviruses (approx 1 micrometer, or 1/1,000 mm in diameter) 
has shaken that paradigm somewhat. Individual virus particles are the 
infectious form of a virus outside the host cell. Unlike bacteria (which are 
about 100 times larger), we cannot see most viruses with a light 
microscope, with the exception of the Pandoraviruses and some large 
virions of the poxvirus family ([link]). 


Pollen 


it f Flu virus 
304 C60 Protein 


Lipids 


Atom 


Plant cell 


Relatives sizes on a logarithmic scale 


0..nm inm 10 nm 100 nm ium 10 um 100 pm 1mm 


Light microscope 


Electron microscope 


The size of a virus is very small relative to the size of 
cells and organelles. 


It was not until the development of the electron microscope in the 1940s 
that scientists got their first good view of the structure of the tobacco 
mosaic virus ({link]) and others. The surface structure of virions can be 
observed by both scanning and transmission electron microscopy, whereas 
the internal structures of the virus can only be observed in images from a 
transmission electron microscope ((link]). 


The ebola virus is shown here as visualized 
through (a) a scanning electron micrograph and 
(b) a transmission electron micrograph. (credit 
a: modification of work by Cynthia Goldsmith, 

CDC; credit b: modification of work by 
Thomas W. Geisbert, Boston University 
School of Medicine; scale-bar data from Matt 
Russell) 


The use of this technology has allowed for the discovery of many viruses of 
all types of living organisms. They were initially grouped by shared 
morphology, meaning their size, shape, and distinguishing structures. Later, 
groups of viruses were classified by the type of nucleic acid they contained, 
DNA or RNA, and whether their nucleic acid was single- or double- 
stranded. More recently, molecular analysis of viral replication cycles has 
further refined their classification. Currently virus classification begins at 
the level of Order, and proceeds to species level taxonomy using this 
scheme. The terms in parentheses are the taxon suffixes for that taxonomic 
level. 

Virus classification 


e Order (-virales) 

e Family (-viridae) 

e Subfamily (-virinae) 

e Genus (-virus) 

e Species (usually XX XX (disease) virus, e.g., Tobacco Mosaic Virus) 


A virion consists of a nucleic-acid core, an outer protein coating, and 
sometimes an outer envelope made of protein and phospholipids derived 
from the host cell. The most visible difference between members of viral 
families is their morphology, which is quite diverse. An interesting feature 
of viral complexity is that the complexity of the host does not correlate to 
the complexity of the virion. Some of the most complex virion structures 
are observed in bacteriophages, viruses that infect the simplest living 
organisms, bacteria. 


Viruses come in many shapes and sizes, but these are consistent and distinct 
for each viral family ({link]). All virions have a nucleic-acid genome 
covered by a protective layer of protein, called a capsid. The capsid is made 
of protein subunits called capsomeres. Some viral capsids are simple 
polyhedral “spheres,” whereas others are quite complex in structure. The 
outer structure surrounding the capsid of some viruses is called the viral 
envelope. All viruses use some sort of glycoprotein to attach to their host 
cells at molecules on the cell called viral receptors. The virus exploits these 
cell-surface molecules, which the cell uses for some other purpose, as a way 
to recognize and infect specific cell types. 


The T4 bacteriophage, which infects the E. coli bacterium, is among the 
most complex virions known; T4 has a protein tail structure that the virus 
uses to attach to the host cell and a head structure that houses its DNA. 


Adenovirus, a nonenveloped animal virus that causes respiratory illnesses 
in humans, uses protein spikes protruding from its capsomeres to attach to 
the host cell. Nonenveloped viruses also include those that cause polio 
(poliovirus), plantar warts (papillomavirus), and hepatitis A (hepatitis A 
virus). Nonenveloped viruses tend to be more robust and more likely to 
survive under harsh conditions, such as the gut. 


Enveloped virions like HIV (human immunodeficiency virus), the causative 
agent in AIDS (acquired immune deficiency syndrome), consist of nucleic 
acid (RNA in the case of HIV) and capsid proteins surrounded by a 
phospholipid bilayer envelope and its associated proteins ({link]). Chicken 
pox, influenza, and mumps are examples of diseases caused by viruses with 
envelopes. Because of the fragility of the envelope, nonenveloped viruses 
are more resistant to changes in temperature, pH, and some disinfectants 
than enveloped viruses. 


Overall, the shape of the virion and the presence or absence of an envelope 
tells us little about what diseases the viruses may cause or what species they 
might infect, but is still a useful means to begin viral classification. 


Bacteriophage T4 


Adenovirus 
Glycoproteins Capsomere 


Tail fibers Reverse 
transcriptase 


Viruses can be complex in shape or 
relatively simple. This figure shows 
three relatively complex virions: the 
bacteriophage T4, with its DNA- 
containing head group and tail fibers 
that attach to host cells; adenovirus, 
which uses spikes from its capsid to 
bind to the host cells; and HIV, which 
uses glycoproteins embedded in its 
envelope to do so. Notice that HIV 
has proteins called matrix proteins, 
internal to the envelope, which help 
stabilize virion shape. HIV is a 
retrovirus, which means it reverse 
transcribes its RNA genome into 
DNA, which is then spliced into the 
host’s DNA. (credit “bacteriophage, 
adenovirus”: modification of work by 
NCBI, NIH; credit “HIV retrovirus”: 
modification of work by NIAID, NIH) 


Unlike all living organisms that use DNA as their genetic material, viruses 
may use either DNA or RNA as theirs. The virus core contains the genome 


or total genetic content of the virus. Viral genomes tend to be small 
compared to bacteria or eukaryotes, containing only those genes that code 
for proteins the virus cannot get from the host cell. This genetic material 
may be single-stranded or double-stranded. It may also be linear or circular. 
While most viruses contain a single segment of nucleic acid, others have 
genomes that consist of several segments. All of these features are used to 
help classify viruses into orders, families, etc. 


DNA viruses have a DNA core. The viral DNA directs the host cell’s 
replication proteins to synthesize new copies of the viral genome and to 
transcribe and translate that genome into viral proteins. DNA viruses cause 
human diseases such as chickenpox, hepatitis B, and some venereal 
diseases like herpes and genital warts. 


RNA viruses contain only RNA in their cores. To replicate their genomes in 
the host cell, the genomes of RNA viruses encode enzymes not found in 
host cells. RNA polymerase enzymes are not as stable as DNA polymerases 
and often make mistakes during transcription. For this reason, mutations, 
changes in the nucleotide sequence, in RNA viruses occur more frequently 
than in DNA viruses. This leads to more rapid evolution and change in 
RNA viruses. For example, the fact that influenza is an RNA virus is one 
reason a new flu vaccine is needed every year; rapid evolution results in 
new flu strains being produced constantly in various parts of the world. 
Human diseases caused by RNA viruses include hepatitis, measles, HIV, 
common cold virus, Ebola and rabies. 


Steps of Virus Infections 


Viruses are specialized parasites, usually only infecting one type of cell or 
one type of organism. A virus must “take over” a cell to replicate. The viral 
replication cycle can produce dramatic biochemical and structural changes 
in the host cell, which may cause cell damage. These changes, called 
cytopathic effects, can change cell functions or even destroy the cell. Some 
infected cells, such as those infected by the common cold virus (rhinovirus), 
die through lysis (bursting) or apoptosis (programmed cell death or “cell 
suicide”), releasing all the progeny virions at once. The symptoms of these 


viral diseases result from the immune response to the virus, which attempts 
to control and eliminate the virus from the body, and from cell damage 
caused by the virus. Many animal viruses, such as HIV (human 
immunodeficiency virus), leave the infected cells of the immune system by 
a process known as budding, where virions leave the cell individually. 
During the budding process, the cell does not undergo lysis and is not 
immediately killed. However, the damage to the cells that HIV infects may 
make it impossible for the cells to function as mediators of immunity, even 
though the cells remain alive for a period of time. Most productive viral 
infections follow similar steps in the ,virus replication cycle : attachment, 
penetration, uncoating, replication, assembly, and release. 


A virus attaches to a specific receptor site on the host-plasma membrane 
through attachment proteins in the capsid or proteins embedded in its 
envelope. The attachment is specific, and typically a virus will only attach 
to cells of one or a few species and only certain cell types within those 
species with the appropriate receptors. 


The nucleic acid of bacteriophages is injected directly into the host cell, 
leaving the capsid outside the cell. Plant and animal viruses can enter their 
cells through endocytosis, in which the plasma membrane surrounds and 
engulfs the entire virus. Some enveloped viruses enter the cell when the 
viral envelope fuses directly with the plasma membrane. Once inside the 
cell, the viral capsid is degraded and the viral nucleic acid is released, 
which then becomes available for replication and transcription. Obviously, 
the naked DNA of a bacteriophage is already available for transcription and 
replication immediately after being injected into the bacterial cell. 


The replication mechanism depends on the viral genome (DNA or RNA). 
DNA viruses usually use host cell proteins and enzymes to make additional 
DNA that is then used to copy the genome or be transcribed to messenger 
RNA (mRNA). The mRNA is then used in protein synthesis. RNA viruses, 
such as the influenza virus, usually use the RNA as a template for synthesis 
of viral genomic RNA and mRNA. The viral mRNA is translated into viral 
enzymes and capsid proteins to assemble new virions ((link]). 


The last stage of viral replication is the release of the new virions into the 
host organism, where they are able to infect adjacent cells and repeat the 


replication cycle. Some viruses are released when the host cell dies and 
other viruses can leave infected cells by budding through the membrane 
without directly killing the cell. 


Influenza virus 
Nucleus 


Receptor 


Epithelial cell ty 
The cell 
engulfs 


: the virus by 
@ Influenza virus becomes endocytosis. 
attached to a target 
epithelial cell. 


® New viral particles are made and Viral MRNA is used to @ Viral contents are released. 
released into the extracellular fluid. make viral proteins. Viral RNA enters the nucleus 
The cell, which is not killed in the where it is replicated by the 
process, continues to make new virus. viral RNA polymerase. 


In influenza virus infection, glycoproteins attach to 
a host epithelial cell. As a result, the virus is 
engulfed. RNA and proteins are made and 
assembled into new virions. 


Lytic and Lysogenic Pathways 


Cell death may be immediate or delayed after attachment and penetration 
by the virus. For example, bacteriophages, viruses that infect bacteria, may 
or may not kill their host immediately. There are two viral replication 
strategies; when the virus kills the host cell it is called the lytic cycle, and 
when the virus does not kill the host but replicates when the host replicates 
it is called the lysogenic cycle ((link)). 


Lytic Attach to host Lysogenic 
& inject DNA 


When triggered, 
the virus 
becomes active 


Host cell and 
viral DNA 
replicate and 
divide 
Host cell lyses and 
viruses are released 


New viral components Viral DNA integrates 
constructed into host 
chromosomes 


The two viral reproductive strategies, the lytic cycle and 
the lysogenic cycle 


Lytic cycle 

The lytic cycle causes death of the host cell and the term refers to the last 
stage of the infection when the cell lyses (breaks open) and releases new 
virions that were produced within the cell. These new virions can infect 
healthy cells and the cycle is repeated ({link]). 


So why haven't all the bacteria in the world been destroy by 
bacteriophages? The answer is natural selection of defense mechanisms by 
bacteria. Mutations of bacterial surface proteins that are not recognized by a 
particular phage allow the bacteria to survive by preventing attachment. 
Without going into detail, bacteria have internal defenses that allow them to 
cut up viral DNA before it can infect the cell. Then one might ask, why 
hasn't all the bacteriophages in the world gone extinct by not being able to 
reproduce. Once again, the answer is natural selection. Viruses mutate to 
bypass the defense mechanisms of the bacteria. This illustrates that the 


parasite-host relationship is in a constant evolutionary duel.Similar co- 
evolutionary strategies characterize the interactions of viruses and animals, 
or viruses and plants. 


Lysogenic cycle 

There is another reason why bacteria are not extinct because of 
bacteriophages. Many bacteriophages do not kill their host but coexist 
within their host, and when this occurs it is called the lysogenic cycle. After 
penetration, the viral DNA or RNA can either be incorporated into the host 
DNA, or the viral genome can be a self-replicating entity. Once this occurs, 
the viral genome is replicated along with the host cell's DNA, but the virus 
does not destroy the cell as it does in the lytic cycle ({link]). However, at 
some point the viral genes are turned on and can trigger the virus to enter 
the lytic cycle and kill the host cell ({link]). Cell starvation or cell damage 
(e.g. from radiation) may trigger a lysogenic infection to turn into a lytic 
infection thereby killing the host cell. The next generation of viruses, 
depending on the host cell condition, can use either of the viral replication 
Strategies, lysogenic or lytic, on the next host. 


Viruses and Disease 


Viruses cause a variety of diseases in animals, including humans, ranging 
from the common cold to potentially fatal illnesses like meningitis ([link]). 
These diseases can be treated by antiviral drugs or by vaccines, but some 
viruses, such as HIV, are capable of avoiding the immune response and 
mutating so as to become resistant to antiviral drugs. 


Overview of Viral Infections 


Encephalitis/ 
meningitis 
- JC virus 


Common cold 

- Rhinoviruses 

- Measles - Parainfluenza virus 
- LCM virus - Respiratory syncytial 
- Arbovirus virus 

- Rabies 


Gingivostomatitis 
- Herpes simplex type 1 


Pharyngitis 
- Adenovirus 
- Epstein-Barr virus 
- Cytomegalovirus 


Cardiovascular 
- Coxsackie B virus 


Hepatitis 
- Hepatitis virus 
types A, B, C, D, andE 


Skin infections 

- Varicella-zoster virus 

- Human herpesvirus 6 

- Smallpox 

- Molluscum contagiosum 
- Human papillomavirus 


- Parvovirus B19 
- Rubella - Herpes simplex type 2 


- Measles - Human papillomavirus 
- Coxsackie A virus - HIV 


Sexually transmitted 
diseases 


Eye infections 

- Herpes simplex virus 
- Adenovirus 

- Cytomegalovirus 


Parotitis -;Pneumonia 


- Influenza virus 
types A and B 

- Parainfluenza 
virus 

- Respiratory 
syncytial virus 

- Adenovirus 

- SARS coronavirus 


Myelitis 
- Poliovirus 
- HTLV-I 


Gastroenteritis 
- Adenovirus 

- Rotavirus 

- Norovirus 

- Astrovirus 

- Coronavirus 


Pancreatitis 
- Coxsackie B virus 


Viruses are the cause of dozens of ailments 
in humans, ranging from mild illnesses to 
serious diseases. (credit: modification of 
work by Mikael Haggstr6m) 


Innate Immunity 


Introduction 

"The organism possesses certain contrivances by means of which the 
immunity reaction, so easily produced by all kinds of cells, is prevented 
from acting against the organism's own elements and so giving rise to 
autotoxins... These contrivances are naturally of the highest importance for 
the existence of the individual." Paul Ehrlich, German immunologist and 
pharmacologist, "On Hemolysins", 1901 


Although other organisms have immune responses of various types, the 
vertebrate immune system is the most sophisticated. The vertebrate immune 
system is a complex multilayered system for defending against external and 
internal threats to the integrity of the body. The system can be divided into 
two types of defense systems: the innate immune system, which is 
nonspecific toward a particular kind of pathogen, and the adaptive immune 
system, which is specific ((link]). Innate immunity relies on physical and 
chemical barriers that work on all pathogens, sometimes called the first line 
of defense. The second line of defense of the innate system includes 
chemical signals that produce inflammation and fever responses as well as 
mobilizing protective cells and other chemical defenses. The adaptive 
immune system mounts a highly specific response to substances and 
organisms that do not belong in the body. The adaptive system takes longer 
to respond and has a memory system that allows it to respond with greater 
intensity should the body re-encounter a pathogen, even years later. That 
memory is the basis for the long-term effectiveness of many vaccines. 


Vertebrate Immunity 


Innate Immune System Adaptive Immune System 
Physical Barriers Internal Defenses 


+ Skin, hair, cilia + Inflammatory response + Antibodies and the humoral immune response 


* Mucus membranes * Complement proteins * Cell-mediated immune response 


* Mucus and chemical secretions * Phagocytic cells * Memory response 
* Digestive enzymes in mouth « Natural killer (NK) cells 


* Stomach acid 


There are two main parts to the vertebrate immune system. The 
innate immune system, which is made up of physical barriers 


and internal defenses, responds to all pathogens. The adaptive 
immune system is highly specific. 


External and Chemical Barriers 


The body has significant physical barriers to potential pathogens. The skin 
contains the protein keratin, which resists physical entry into cells. Other 
body surfaces, particularly those associated with body openings, are 
protected by the mucous membranes. The sticky mucus provides a physical 
trap for pathogens, preventing their movement deeper into the body. Some 
openings of the body, such as the nose and ears, are protected by hairs that 
catch pathogens, and the mucous membranes of the upper respiratory tract 
have cilia that constantly sweep pathogens trapped in the mucus coat up to 
the mouth. The skin and mucous membranes also create a chemical 
environment that is hostile to many microorganisms. The surface of the skin 
is acidic, which prevents bacterial growth. Saliva, mucus, and the tears of 
the eye contain an enzyme that breaks down bacterial cell walls. The 
stomach secretions create a highly acidic environment, which kills many 
pathogens entering the digestive system. 


Finally, the surface of the body and the lower digestive system have a 
community of commensal microorganisms such as bacteria, archaea, and 
fungi (the microbiome) that coexist without harming the body. There is 
evidence that these organisms are highly beneficial to their host, combating 
disease-causing organisms and outcompeting them for nutritional resources 
provided by the host body. Despite these defenses, pathogens may enter the 
body through skin abrasions or punctures, or by collecting on mucosal 
surfaces in large numbers that overcome the protections of mucus or cilia. 


Internal Defenses 


If pathogens defeat these defenses and enter the body, the innate immune 
system responds with a variety of internal defenses. These include the 
inflammatory response, phagocytosis, natural killer cells, and the 


complement system. White blood cells in the blood and lymph recognize 
pathogens as foreign to the body. A white blood cell is larger than a red 
blood cell, is nucleated, and is typically able to move using amoeboid 
locomotion. Because they can move on their own, white blood cells can 
leave the blood to go to infected tissues. For example, a monocyte is a type 
of white blood cell that circulates in the blood and lymph and develops into 
a macrophage after it moves into infected tissue. A macrophage is a large 
phagocytic cell that engulfs and devours foreign particles and pathogens. 


Once a pathogen is recognized as foreign and devoured by a macrophage, 
chemicals called cytokines are released. A cytokine is a chemical 
messenger that regulates cell differentiation (form and function), 
proliferation (production), and gene expression to produce a variety of 
immune responses. Approximately 40 types of cytokines exist in humans. 
In addition to being released from white blood cells after pathogen 
recognition, cytokines are also released by the infected cells and bind to 
nearby uninfected cells, inducing those cells to release cytokines. This 
positive feedback loop results in a burst of cytokine production. 


One class of early-acting cytokines is the interferons, which are released by 
infected cells as a warning to nearby uninfected cells. An interferon is a 
small protein that signals a viral infection to other cells. The interferons 
stimulate uninfected cells to produce compounds that interfere with viral 
replication. Interferons also activate macrophages and other cells. 


The Inflammatory Response and Phagocytosis 


The first cytokines to be produced encourage inflammation, a localized 
redness, swelling, heat, and pain. Inflammation is a response to physical 
trauma, such as a cut or a blow, chemical irritation, and infection by 
pathogens (viruses, bacteria, or fungi). The chemical signals that trigger an 
inflammatory response enter the extracellular fluid and cause capillaries to 
dilate (expand) and capillary walls to become more permeable, or leaky. 
The serum and other compounds leaking from capillaries cause swelling of 
the area, which in turn causes pain. Various kinds of white blood cells are 
attracted by the cytokines released at the area of inflammation. The types of 


white blood cells that arrive at an inflamed site depend on the nature of the 
injury or infecting pathogen. For example, a neutrophil is an early arriving 
white blood cell that engulfs and digests pathogens. Neutrophils are the 
most abundant white blood cells of the immune system ((Link]). 
Macrophages follow neutrophils and take over the phagocytosis function 
and are involved in cleaning up cell debris and pathogens. 


White blood cells 
(leukocytes) release 
chemicals to stimulate 
the inflammatory 
response following a 
cut in the skin. 


Cytokines also send feedback to cells of the nervous system to bring about 
the overall symptoms of feeling sick, which include lethargy, muscle pain, 
and nausea. Cytokines can thus increase the core body temperature, causing 
a fever. The elevated temperatures of a fever inhibit the growth of 
pathogens and speed up cellular repair processes. For these reasons, 
suppression of fevers should be limited to those that are dangerously high. 


Natural Killer Cells 


A lymphocyte is a white blood cell that contains a large nucleus ((link]). 
Most lymphocytes are associated with the adaptive immune response, but a 
class of lymphocytes known as natural killer cells are part of the innate 
immune system. Unlike other white blood cells that attack invading bacteria 
or fungi, natural killer (NK) cell is a lymphocyte. Natural killer cells kill 
body cells that are infected with viruses (or cancerous cells). NK cells 
identify intracellular infections, especially from viruses, and attack the 
infected cells, destroying them so that they cannot release more viruses. 


eo 


5 yum 
i, 


Lymphocytes, such 
as NK cells, are 
characterized by 
their large nuclei 

that actively absorb 
Wright stain and 
therefore appear 

dark colored under 
a microscope. 
(credit: scale-bar 
data from Matt 
Russell) 


Mast cell Natural killer cell Monocyte Macrophage Neutrophil 


Cells involved in the innate immune response include mast 
cells, natural killer cells, and white blood cells, such as 
monocytes, macrophages and neutrophils. 


Complement 


An array of approximately 20 types of proteins, called a complement 
system, is also activated by infection or the activity of the cells of the 
adaptive immune system and functions to destroy extracellular pathogens. 
Liver cells and macrophages synthesize inactive forms of complement 
proteins continuously; these proteins are abundant in the blood serum and 
are capable of responding immediately to infecting microorganisms. The 
complement system is so named because it is complementary to the innate 
and adaptive immune system. Complement proteins bind to the surfaces of 
microorganisms and are particularly attracted to pathogens that are already 
tagged by the adaptive immune system. This “tagging” involves the 
attachment of specific proteins called antibodies (discussed in detail later) 
to the pathogen. When they attach, the antibodies change shape providing a 
binding site for one of the complement proteins. After the first few 
complement proteins bind, a cascade of binding in a specific sequence of 
proteins follows in which the pathogen rapidly becomes coated in 
complement proteins. 


Complement proteins perform several functions, one of which is to serve as 
a marker to indicate the presence of a pathogen to phagocytic cells and 
enhance engulfment. Certain complement proteins can combine to open 


pores in microbial plasma membranes, causing ion leakage and lysis of the 
microbial cells. 


Adaptive Immunity 


Introduction 

"An immune system of enormous complexity is present in all vertebrate 
animals. When we place a population of lymphocytes from such an animal 
in appropriate tissue culture fluid, and when we add an antigen, the 
lymphocytes will produce specific antibody molecules, in the absense of 
any nerve cells. I find it astonishing that the immune system embodies a 
degree of complexity which suggests some more or less superficial though 
striking analogies with human language, and that this cognitive system has 
evolved and functions without assistance of the brain." Niels K. Jerne, 
Danish immunologist, "The Generative Grammar of the Immune System", 
Nobel Lecture, 1984 


The adaptive, or acquired, immune response takes days or even weeks to 
become established—much longer than the innate response; however, 
adaptive immunity is more specific to an invading pathogen. Adaptive 
immunity is an immunity that occurs after exposure to an antigen either 
from a pathogen or a vaccination. An antigen is a molecule that stimulates 
a response in the immune system. This part of the immune system is 
activated when the innate immune response is insufficient to control an 
infection. In fact, without information from the innate immune system, the 
adaptive response could not be mobilized. There are two types of adaptive 
responses: the cell-mediated immune response, which is controlled by 
activated T cells, and the humoral immune response, which is controlled 
by activated B cells and antibodies. Activated T and B cells, which 
specifically bind to molecules from the invading pathogen, attack the 
pathogen specifically. These cells can kill pathogens directly, or they can 
secrete antibodies that enhance the phagocytosis of pathogens and disrupt 
the infection. Adaptive immunity also involves a memory to give the host 
long-term protection from reinfection with the same type of pathogen; on 
reexposure, this host memory will facilitate a rapid and powerful response. 


B and T Cells 


Lymphocytes, which are white blood cells, are formed with other blood 
cells in the red bone marrow. The two types of lymphocytes of the adaptive 


immune response are B and T cells ({link]). Whether an immature 
lymphocyte becomes a B cell or T cell depends on where in the body it 
matures. The B cells remain in the bone marrow to mature (hence the name 
“B” for “bone marrow”), while T cells migrate to the thymus, where they 
mature (hence the name “T” for “thymus”). 


Maturation of a B or T cell involves becoming immunocompetent, meaning 
that it can recognize, by binding, a specific molecule or antigen (discussed 
below). During the maturation process, B and T cells that bind too strongly 
to the body’s own cells are eliminated in order to minimize an immune 
response against the body’s own tissues. Those cells that react weakly or 
not at all to the body’s own cells, but have highly specific receptors on their 
cell surfaces that allow them to recognize a foreign molecule, or antigen, 
remain. This process occurs during fetal development and continues 
throughout life. The specificity of this receptor is determined by the 
genetics of the individual and is present before a foreign molecule is 
introduced to the body or encountered. Thus, it is genetics and not 
experience that initially provides a vast array of cells, each capable of 
binding to a different specific foreign molecule. Once they are 
immunocompetent, the T and B cells will migrate to the spleen and lymph 
nodes where they will remain until they are called on during an infection. B 
cells are involved in the humoral immune response, which targets 
pathogens found in blood and lymph, and T cells are involved in the cell- 
mediated immune response, which targets infected body cells. 


This scanning electron 
micrograph shows a T 
lymphocyte. T and B 
cells are indistinguishable 
by light microscopy but 
can be differentiated 
experimentally by 
probing their surface 
receptors. (credit: 
modification of work by 
NCI; scale-bar data from 
Matt Russell) 


Humoral Immune Response 


As mentioned, an antigen is a molecule that stimulates a response in the 
immune system. B cells participate in a chemical response to new antigens 
by producing specific antibodies that circulate throughout the body and 
bind with the antigen whenever it is encountered. This is known as the 
humoral immune response, because the active molecule is secreted into 
the body fluids, or "humours". As discussed, during maturation of B cells, a 
set of highly specific B cells are produced that have many antigen receptor 
molecules in their membrane ((link]). 


Antigens 


Antigen 
y Antigen-binding site 


B cell receptors are 
embedded in the 
membranes of B 
cells and bind a 

variety of antigens 

through their 
variable regions. 


Each B cell has only one kind of antigen receptor, which makes every B cell 
different. Once the B cells mature in the bone marrow, they migrate to 
lymph nodes or other lymphatic organs. When a B cell encounters the 
antigen that binds to its receptor, the antigen molecule is brought into the 
cell by endocytosis. It is digested in the lysosomes, and fragments of the 
foreign molecule are then displayed on the surface of the B cell. These 
displayed molecules can activate other cells as part of the immune response. 
When this process is complete, the B cell is sensitized. In most cases, the 
sensitized B cell must then encounter a specific kind of T cell, called a 
helper T cell, before it is activated. The helper T cell must already have 
been activated through an encounter with the antigen (discussed below). 


The helper T cell binds to the displayed antigen fragments on the B cell, 
and is activated to release cytokines that induce the B cell to divide rapidly. 
This generates thousands of identical (clonal) B cells. These daughter cells 


have two possible fates: they can become either plasma cells or memory B 
cells. The plasma cells produce and secrete large quantities of antibody 
molecules, up to 100 million molecules per hour, . An antibody, also 
known as an immunoglobulin (Ig), is a protein that is produced by plasma 
cells after stimulation by an antigen. Antibodies are the agents of humoral 
immunity. Antibodies occur in the blood, in gastric and mucus secretions, 
and in breast milk. Antibodies in these bodily fluids can bind pathogens and 
mark them for destruction by phagocytes before they can infect cells. The 
memory B cells become quiescent, and only become reactivated after 
another later encounter with the antigen. This can be caused by a reinfection 
by the same bacteria or virus, and activation of the memory cells again 
results in a new population of antibody-producing plasma cells to fight the 
re-infection. 


These antibodies circulate in the blood stream and lymphatic system and 
bind with the antigen whenever it is encountered. The binding can fight 
infection in several ways. Antibodies can bind to viruses or bacteria and 
interfere with the chemical interactions required for them to infect or bind 
to other cells. The antibodies may create bridges between different particles 
containing antigenic sites clumping them all together and preventing their 
proper functioning. The antigen-antibody complex stimulates the 
complement system described previously, destroying the cell bearing the 
antigen. Phagocytic cells, such as those already described, are attracted by 
the antigen-antibody complexes, and phagocytosis is enhanced when the 
complexes are present. Finally, antibodies stimulate inflammation, and their 
presence in mucus and on the skin prevents pathogen attack. 


Antibodies coat extracellular pathogens and neutralize them by blocking 
key sites on the pathogen that enhance their infectivity (such as receptors 
that “dock” pathogens on host cells) ({link]). Antibody neutralization can 
prevent pathogens from entering and infecting host cells. The neutralized 
antibody-coated pathogens can then be filtered by the spleen and destroyed. 


Antibodies also mark pathogens for destruction by phagocytic cells, such as 
macrophages or neutrophils, in a process called opsonization. In a process 
called complement fixation, some antibodies provide a place for 


complement proteins to bind. The combination of antibodies and 
complement promotes rapid clearing of pathogens. 


The production of antibodies by plasma cells in response to an antigen is 
called active immunity and describes the host’s active immune response to 
an infection or to a vaccination. There is also a passive immune response 
where antibodies come from an outside source, instead of the individual’s 
own plasma cells, and are introduced into the host. For example, antibodies 
circulating in a pregnant woman’s body move across the placenta into the 
developing fetus. The child benefits from the presence of these antibodies 
for up to several months after birth. In addition, a passive immune response 
is possible by injecting antibodies into an individual in the form of an 
antivenom to a snake-bite toxin or antibodies in blood serum to help fight a 
hepatitis infection. This gives immediate protection since the body does not 
need the time required to mount its own response. 


(a) Neutralization Antibodies prevent a virus or toxic protein 
from binding their target. 


Antibody 


Virus 


Diptheria toxin 
(b) Opsonization A pathogen tagged by antibodies is consumed 
by a macrophage or neutrophil. 


Macrophage 


Pathogen 


(c) Complement activation Antibodies attached to the surface 
of a pathogen cell activate the complement system. 


Pores formed 
by complement 


Antibodies may inhibit infection 
by (a) preventing the antigen 
from binding its target, (b) 
tagging a pathogen for 
destruction by macrophages or 
neutrophils, or (c) activating the 
complement cascade. 


Cell-Mediated Immunity 


Unlike B cells, T lymphocytes are unable to recognize pathogens without 
assistance. Instead, dendritic cells and macrophages first engulf and digest 


pathogens into hundreds or thousands of antigens. Then, an antigen- 
presenting cell (APC) detects, engulfs, and informs the adaptive immune 
response about an infection. When a pathogen is detected, these APCs will 
engulf and break it down through phagocytosis. Antigen fragments will 
then be transported to the surface of the APC, where they will serve as an 
indicator to other immune cells. A dendritic cell is an immune cell that 
mops up antigenic materials in its surroundings and presents them on its 
surface. Dendritic cells are located in the skin, the linings of the nose, lungs, 
stomach, and intestines. These positions are ideal locations to encounter 
invading pathogens. Once they are activated by pathogens and mature to 
become APCs they migrate to the spleen or a lymph node. Macrophages 
also function as APCs. In all cases the foreign antigen is digested inside the 
cell, and fragments of the antigen are then displayed on the surface of the 
APC. 


(4) Abacterium 
engulfed by a 
macrophage is 
encased ina 


vacuole. (2) Lysosomes fuse 


with the vacuole 
and digest the 


Antigen bacterium. 


Macrophage 


(3) Antigens from digested 
bacterium are presented with 
MHC II on the cell surface. 


An antigen-presenting cell 
(APC), such as a macrophage, 
engulfs a foreign antigen, 
partially digests it in a lysosome, 
and then displays it at the cell 
surface. Lymphocytes of the 
adaptive immune response must 
interact with these displayed 
fragments, bound to a specific 


protein on the APC cell surface, 
in order to mature into 
functional immune cells. 


T cells have many functions. Some respond to APCs of the innate immune 
system and indirectly induce immune responses by releasing cytokines. 
Others stimulate B cells to start the humoral response as described 
previously. Another type of T cell detects APC signals and directly kills the 
infected cells, while some are involved in suppressing inappropriate 
immune reactions to harmless or “self” antigens. 


There are two main types of T cells: helper T lymphocytes (T}) and the 
cytotoxic T lymphocytes (Tc). The Ty lymphocytes function indirectly to 
tell other immune cells about potential pathogens. Ty lymphocytes 
recognize specific antigens presented by the MHC class II complexes of 
APCs. There are two populations of Ty cells: Ty1 and Ty2. Ty1 cells 
secrete cytokines to enhance the activities of macrophages and other T 
cells. Ty2 cells stimulate naive B cells to secrete antibodies. Whether a Ty1 
or a T}y2 immune response develops depends on the specific types of 
cytokines secreted by cells of the innate immune system, which in turn 
depends on the nature of the invading pathogen. 


Cytotoxic T cells (T-) are the key component of the cell-mediated part of 
the adaptive immune system and attack and destroy infected cells. Tc cells 
are particularly important in protecting against viral infections; this is 
because viruses replicate within cells where they are shielded from 
extracellular contact with circulating antibodies. Once activated, the Tc 
creates a large clone of cells with one specific set of cell-surface receptors, 
as in the case with proliferation of activated B cells. As with B cells, the 
clone includes active T¢ cells and inactive memory T¢ cells. The resulting 
active Tc cells then identify infected host cells. Because of the time 
required to generate a population of clonal T and B cells, there is a delay in 
the adaptive immune response compared to the innate immune response. 


Tc cells attempt to identify and destroy infected cells before the pathogen 
can replicate and escape, thereby halting the progression of intracellular 
infections. Tc cells also support NK lymphocytes to destroy early cancers. 
Cytokines secreted by the Ty1 response that stimulates macrophages also 
stimulate Tc cells and enhance their ability to identify and destroy infected 
cells and tumors. A summary of how the humoral and cell-mediated 
immune responses are activated appears in [link]. 


B plasma cells and T¢ cells are collectively called effector cells because 


they are involved in “effecting” (bringing about) the immune response of 
killing pathogens and infected host cells. 


Bacterium 


Antigen 


Macrophage 


Antigens from digested 

bacterium are presented with 

MHC II on the cell surface. In response to cytokines, 
the T cell clones itself. 


Activated 


Humoral 
helper T cell 


immune 
response 


2 om, cell clones itself 


Cell-mediated 
immune 
response 


co Cytokines 


Bee T cell becomes 
Cytokines activate cytotoxic. 
B cells and T cells 


A helper T cell becomes activated by binding to an antigen 
presented by an APC via the MHCII receptor, causing it to 
release cytokines. Depending on the cytokines released, this 
activates either the humoral or the cell-mediated immune 
response. 


Immunological Memory 


The adaptive immune system has a memory component that allows for a 
rapid and large response upon reinvasion of the same pathogen. During the 
adaptive immune response to a pathogen that has not been encountered 
before, known as the primary immune response, plasma cells secreting 
antibodies and differentiated T cells increase, then plateau over time. As B 
and T cells mature into effector cells, a subset of the naive populations 
differentiates into B and T memory cells with the same antigen specificities 
({link]). A memory cell is an antigen-specific B or T lymphocyte that does 
not differentiate into an effector cell during the primary immune response, 
but that can immediately become an effector cell on reexposure to the same 
pathogen. As the infection is cleared and pathogenic stimuli subside, the 
effectors are no longer needed and they undergo apoptosis. In contrast, the 
memory cells persist in the circulation. 


ee B cell receptor 
Antigen on 

bacterium 
B cell 


@ 


Memory B cells Plasma cells 


After initially binding an antigen to 
the B cell receptor, a B cell 
internalizes the antigen and 

presents it on MHC class IT. A 
helper T cell recognizes the MHC 
class IT- antigen complex and 
activates the B cell. As a result, 
memory B cells and plasma cells 
are made. 


If the pathogen is never encountered again during the individual’s lifetime, 
B and T memory cells will circulate for a few years or even several decades 
and will gradually die off, having never functioned as effector cells. 
However, if the host is re-exposed to the same pathogen type, circulating 
memory cells will immediately differentiate into plasma cells and T¢ cells 
without input from APCs or Ty cells. This is known as the secondary 


immune response. One reason why the adaptive immune response is 
delayed is because it takes time for naive B and T cells with the appropriate 
antigen specificities to be identified, activated, and proliferate. On 
reinfection, this step is skipped, and the result is a more rapid production of 
immune defenses. Memory B cells that differentiate into plasma cells 
produce antibody at a level that is tens to hundreds-fold greater than during 
the primary response ({link]). This rapid and dramatic antibody response 
may stop the infection before it can even become established, and the 
individual may not realize they had been exposed. 


Antibody concentration ——» 


Primary immune Secondary immune 
response response 


Time ——> 


In the primary response to 
infection, antibodies are 
secreted first from plasma 
cells. Upon re-exposure to 
the same pathogen, memory 
cells differentiate into 
antibody-secreting plasma 
cells that output a greater 
amount of antibody for a 
longer period of time. 


Vaccination is based on the knowledge that exposure to noninfectious 
antigens, derived from known pathogens, generates a mild primary immune 


response. The immune response to vaccination may not be perceived by the 
host as illness but still confers immune memory. When exposed to the 
corresponding pathogen to which an individual was vaccinated, the reaction 
is similar to a secondary exposure. Because each reinfection generates more 
memory cells and increased resistance to the pathogen, some vaccine 
courses involve one or more booster vaccinations to mimic repeat 
exposures. 


The Lymphatic System 


Lymph is the watery fluid that bathes tissues and organs and contains 
protective white blood cells but does not contain erythrocytes. Lymph 
moves about the body through the lymphatic system, which is made up of 
vessels, lymph ducts, lymph glands, and organs, such as tonsils, adenoids, 
thymus, and spleen. 


Although the immune system is characterized by circulating cells 
throughout the body, the regulation, maturation, and intercommunication of 
immune factors occur at specific sites. The blood circulates immune cells, 
proteins, and other factors through the body. Approximately 0.1 percent of 
all cells in the blood are leukocytes, which include monocytes (the 
precursor of macrophages) and lymphocytes. Most cells in the blood are red 
blood cells. Cells of the immune system can travel between the distinct 
lymphatic and blood circulatory systems, which are separated by interstitial 
space, by a process called extravasation (passing through to surrounding 
tissue). 


Recall that cells of the immune system originate from stem cells in the bone 
marrow. B cell maturation occurs in the bone marrow, whereas progenitor 
cells migrate from the bone marrow and develop and mature into naive T 
cells in the organ called the thymus. 


On maturation, T and B lymphocytes circulate to various destinations. 
Lymph nodes scattered throughout the body house large populations of T 
and B cells, dendritic cells, and macrophages ([link]). Lymph gathers 
antigens as it drains from tissues. These antigens then are filtered through 
lymph nodes before the lymph is returned to circulation. APCs in the lymph 


nodes capture and process antigens and inform nearby lymphocytes about 
potential pathogens. 


Afferent lymphatic 
vessel 


Lymph 


Efferent lymphatic 
vessel 


(b) 


(a) Lymphatic vessels carry a clear fluid called 
lymph throughout the body. The liquid passes 
through (b) lymph nodes that filter the lymph 
that enters the node through afferent vessels 
and leaves through efferent vessels; lymph 
nodes are filled with lymphocytes that purge 
infecting cells. (credit a: modification of work 
by NIH; credit b: modification of work by NCI, 
NIH) 


The spleen houses B and T cells, macrophages, dendritic cells, and NK cells 
({link]). The spleen is the site where APCs that have trapped foreign 
particles in the blood can communicate with lymphocytes. Antibodies are 
synthesized and secreted by activated plasma cells in the spleen, and the 
spleen filters foreign substances and antibody-complexed pathogens from 
the blood. Functionally, the spleen is to the blood as lymph nodes are to the 
lymph. 


The spleen functions to 
immunologically filter the 
blood and allow for 
communication between cells 
corresponding to the innate 
and adaptive immune 
responses. (credit: 
modification of work by NCI, 
NIH) 


Besides its close ties to and functions with the immune system, the 
lymphatic system also serves a couple of other important functions. First, 
the vessels of lymphatic system help absorb excess lymph from body 
tissues and returns that lymph to the circulatory system via the lymphatic 
ducts. This helps the body maintain fluid balance. The second function 
deals with the absorption of lipids during digestion. The lymph vessels 
located around the small intestine absorb the lacteals from the lumen of the 
intestine and transport the lacteals to the circulatory system via the 
lymphatic ducts. In this case the lymphatic system acts as a shuttle for 
digested fats from the digestive system to the circulatory system. 


Immune Tolerance 


The immune system has to be regulated to prevent wasteful, unnecessary 
responses to harmless substances, and more importantly, so that it does not 
attack “self.” The acquired ability to prevent an unnecessary or harmful 
immune response to a detected foreign substance known not to cause 
disease, or self-antigens, is described as immune tolerance. The primary 
mechanism for developing immune tolerance to self-antigens occurs during 
the selection for weakly self-binding cells during T and B lymphocyte 
maturation. There are populations of T cells that suppress the immune 
response to self-antigens and that suppress the immune response after the 
infection has cleared to minimize host cell damage induced by 
inflammation and cell lysis. Immune tolerance is especially well developed 
in the mucosa of the upper digestive system because of the tremendous 
number of foreign substances (such as food proteins) that APCs of the oral 
cavity, pharynx, and gastrointestinal mucosa encounter. Immune tolerance 
is brought about by specialized APCs in the liver, lymph nodes, small 
intestine, and lung that present harmless antigens to a diverse population of 
regulatory T (Tyeg) cells, specialized lymphocytes that suppress local 
inflammation and inhibit the secretion of stimulatory immune factors. The 
combined result of Tyeg cells is to prevent immunologic activation and 
inflammation in undesired tissue compartments and to allow the immune 
system to focus on pathogens instead. 


Urinary System 


Introduction 

" What is man, when you come to think upon him, but a minutely set, 
ingenious machine for turning, with infinite artfulness, the red wine of 
Shiraz into urine?" Baroness Karen Blixen, in The Dreamers, 1943 


Osmoregulation and Osmotic Balance 


Osmosis is the diffusion of water across a membrane in response to osmotic 
pressure caused by differences in the solute molecules on either side of the 
membrane. Osmoregulation is the active homeostatic process of the water 
content of an organism, involving movement of solutes across membranes 
so that water moves in response to the ion concentration . It might be 
beneficial to review osmosis here - [link]. Osmo regulation involves control 
of the water and solute content of all the fluids in the animal body. There 
are three general fluid pools in the typical animal: the blood plasma, the 
cytosol within cells, and the interstitial fluid (the fluid that exists in the 
spaces between cells and tissues of the body). See [link] for a review of 
how solute concentrations affect the movement of water across plasma 
membranes. 


Hypertonic Isotonic Hypotonic 
HO 
—e 


Cells placed in a hypertonic environment 
tend to shrink due to loss of water. In a 
hypotonic environment, cells tend to swell 
due to intake of water. The blood 


maintains an isotonic environment so that 
cells neither shrink nor swell. (credit: 
Mariana Ruiz Villareal) 


Need for Osmoregulation 


The body does not exist in isolation. There is a constant input of water and 
electrolytes into the system; osmoregulation is thus a constant process. 
Biological systems constantly interact and exchange water and nutrients 
with the environment by way of consumption of food and water and 
through excretion in the form of sweat, urine, and feces. Without a 
mechanism to regulate osmotic pressure, or when a disease damages this 
mechanism, there is a tendency to accumulate toxic waste and either gain or 
lose water, which can have dire consequences. 


Mammalian systems have evolved to regulate not only the overall osmotic 
pressure across membranes, but also specific concentrations of important 
electrolytes in the three major fluid compartments: blood plasma, 
extracellular fluid, and intracellular fluid. Since osmotic pressure is 
regulated by the movement of water across membranes, the volume of the 
fluid compartments can also change temporarily. Because blood plasma is 
one of the fluid components, osmotic pressures have a direct bearing on 
blood pressure. 


Transport of Electrolytes across Plasmal Membranes 


Electrolytes, such as sodium chloride, ionize in water, meaning that they 
dissociate into their component ions. In water, sodium chloride (NaCl), 
dissociates into the sodium ion (Na‘) and the chloride ion (CI-). The most 
important ions, whose concentrations are very closely regulated in body 
fluids, are the cations sodium (Na*), potassium (K*), calcium (Ca‘*?), 
magnesium (Mg*?), and the anions chloride (CI’), carbonate (CO3°), 


bicarbonate (HCO3)), and phosphate(PO3°). Electrolytes are lost from the 
body during urination and perspiration. For this reason, athletes are 
encouraged to replace electrolytes and fluids during periods of increased 
activity and perspiration. 


Osmotic pressure is influenced by the concentration of solutes in a solution. 
It is directly proportional to the concentration of solute atoms or molecules, 
and not dependent on the size of the solute molecules. Because some 
compounds (known as electrolytes) dissociate into their component ions, 
they add more solute particles into the solution and have a greater effect on 
osmotic pressure, per mass than compounds that do not dissociate in water, 
such as glucose. 


Water can pass through membranes by passive diffusion. If electrolyte ions 
could passively diffuse across membranes, it would be impossible to 
maintain specific concentrations of ions in each fluid compartment 
therefore they require special mechanisms to cross the semi-permeable 
membranes in the body. This movement can be accomplished by facilitated 
diffusion and active transport. Facilitated diffusion requires protein-based 
channels for moving the solute. Active transport requires energy in the form 
of ATP conversion, carrier proteins, or pumps in order to move ions against 
the concentration gradient. 


Osmoregulators and Osmoconformers 


Persons lost at sea without any fresh water to drink are at risk of severe 
dehydration because the human body cannot adapt to drinking seawater, 
which is hypertonic in comparison to body fluids. Organisms such as 
goldfish that can tolerate only a relatively narrow range of salinity are 
referred to as stenohaline. About 90 percent of all bony fish are restricted to 
either freshwater or seawater. They are incapable of osmotic regulation in 
the opposite environment. It is possible, however, for a few fishes like 
salmon to spend part of their life in fresh water and part in sea water. 
Organisms like the salmon that can tolerate a relatively wide range of 
salinity are referred to as euryhaline organisms. This is possible because 
some fish have evolved osmoregulatory mechanisms to survive in all kinds 


of aquatic environments. When they live in fresh water, their bodies tend to 
take up water because the environment is relatively hypotonic, as illustrated 
in [link]a. In such hypotonic environments, these fish do not drink much 
water. Instead, they pass a lot of very dilute urine, and they achieve 
electrolyte balance by active transport of salts through the gills. When they 
move to a hypertonic marine environment, these fish start drinking sea 
water; they excrete the excess salts through their gills and their urine, as 
illustrated in [link]b. Most marine invertebrates, on the other hand, may be 
isotonic with sea water; these are known as osmoconformers. Their body 
fluid concentrations conform to changes in seawater concentration. 
Cartilaginous fishes’ salt composition of the blood is similar to bony fishes; 
however, the blood of sharks contains the organic compounds urea and 
trimethylamine oxide (TMAO). This does not mean that their electrolyte 
composition is similar to that of sea water. They achieve isotonicity with the 
sea by storing large concentrations of urea. These animals that secrete urea 
are called ureotelic animals. TMAO stabilizes proteins in the presence of 
high urea levels, preventing the disruption of peptide bonds that would 
occur in other animals exposed to similar levels of urea. Sharks have a 
rectal gland which secretes salt and assists in osmoregulation. 


Absorbs water through skin 


Actively takes up ions 
through gills 


Drinks little 
water 


===> Movement of water 
===> Movement of ions 
Excretes dilute urine 


(a) Osmoregulation in a freshwater environment 


Loses water through skin 


Drinks ample 
water 


Direction of ion Direction of water 
movement movement 
(Na*,K*,Ch) 


Excretes ions through gills Excretes concentrated urine 


(b) Osmoregulation in a saltwater environment 


Fish are osmoregulators, but must use different mechanisms to 
survive in (a) freshwater or (b) saltwater environments. (credit: 
modification of work by Duane Raver, NOAA) 


Kidneys and Osmoregulatory Organs 


Although the kidneys are the major osmoregulatory organ, the skin and 
lungs also play a role in the process. Water and electrolytes are lost through 
sweat glands in the skin, which helps moisturize and cool the skin surface, 
while the lungs expel a small amount of water in the form of mucous 
secretions and via evaporation of water vapor. 


Kidneys: The Main Osmoregulatory Organ 


The kidneys, illustrated in [link], are a pair of bean-shaped structures that 
are located just below and posterior to the liver in the peritoneal cavity. The 
adrenal glands sit on top of each kidney. Kidneys filter blood and purify it. 
All the blood in the human body is filtered many times a day by the 
kidneys; these organs use up almost 25 percent of the oxygen absorbed 
through the lungs to perform this function. The filtrate coming out of the 
kidneys is called urine. 


Renal artery 


Adrenal 
gland 


Kidney Renal vein 


Ureter 
Renal 


pelvis 


Bladder 


Urethra 


Kidneys filter the blood, 
producing urine that is stored in 
the bladder prior to elimination 

through the urethra. (credit: 
modification of work by NCI) 


Kidney Structure 


Externally, the kidneys are surrounded by three layers, illustrated in [Link]. 
The outermost layer is a tough connective tissue layer called the renal 
fascia. The second layer is called the perirenal fat capsule, which helps 
anchor the kidneys in place. The third and innermost layer is the renal 
capsule. Internally, the kidney has three regions—an outer cortex, a medulla 
in the middle, and the renal pelvis in the region called the hilum of the 
kidney. The hilum is the concave part of the bean-shape where blood 
vessels and nerves enter and exit the kidney; it is also the point of exit for 
the ureters. The renal cortex is granular due to the presence of nephrons— 
the functional unit of the kidney. The medulla consists of multiple 
pyramidal tissue masses, called the renal pyramids. In between the 
pyramids are spaces called renal columns through which the blood vessels 
pass. The tips of the pyramids, called renal papillae, point toward the renal 
pelvis. There are, on average, eight renal pyramids in each kidney. The 
renal pyramids along with the adjoining cortical region are called the lobes 
of the kidney. The renal pelvis leads to the ureter on the outside of the 
kidney. On the inside of the kidney, the renal pelvis branches out into two or 
three extensions called the major calyces, which further branch into the 
minor calyces. The ureters are urine-bearing tubes that exit the kidney and 
empty into the urinary bladder. 


Capillaries 


Arteriole 


Venule 
; Renal pyramid 
Renal vein 
Renal artery 


Renal pelvis 


Medulla 
Ureter 


Renal fascia and cortex Cortex 


The internal structure of the kidney is shown. 
(credit: modification of work by NCI) 


Because the kidney filters blood, its network of blood vessels is an 
important component of its structure and function. The arteries, veins, and 
nerves that supply the kidney enter and exit at the renal hilum. Renal blood 
supply starts with the branching of the aorta into the renal arteries and ends 
with the exiting of the renal veins to join the inferior vena cava. 


As mentioned previously, the functional unit of the kidney is the nephron, 
illustrated in [link]. Each kidney is made up of over one million nephrons 
that dot the renal cortex, giving it a granular appearance when sectioned 
sagittally. A nephron consists of three parts—a renal corpuscle, a renal 
tubule, and the associated capillary network, which originates from the 
arteries that supply blood to the kidney. 


Proximal convoluted 


Nephron tubule Peritubular 


capillaries 


Distal 
convoluted 
tubule 


Efferent 
arteriole 


i= 
/ Medulla 


capsule 


Afferent 
arteriole 


The nephron is the functional unit of the kidney. The 
glomerulus and convoluted tubules are located in the 
kidney cortex, while collecting ducts are located in the 
pyramids of the medulla. (credit: modification of work by 
NIDDK) 


Renal Corpuscle 


The renal corpuscle, located in the renal cortex, is made up of a network of 
capillaries known as the glomerulus and the capsule, a cup-shaped chamber 
that surrounds it, called the glomerular or Bowman's capsule. 


Renal Tubule 


The renal tubule is a long and convoluted structure that emerges from the 
glomerulus and can be divided into three parts based on function. The first 
part is called the proximal convoluted tubule (PCT) due to its proximity 
to the glomerulus; it stays in the renal cortex. The second part is called the 
loop of Henle, or nephritic loop, because it forms a loop (with descending 
and ascending limbs) that goes through the renal medulla. The third part of 
the renal tubule is called the distal convoluted tubule (DCT) and this part 
is also restricted to the renal cortex. The DCT, which is the last part of the 
nephron, connects and empties its contents into collecting ducts that line the 
medullary pyramids. The collecting ducts amass contents from multiple 
nephrons and fuse together as they enter the papillae of the renal medulla. 


Capillary Network within the Nephron 


The capillary network that originates from the renal arteries supplies the 
nephron with blood that needs to be filtered. The branch that enters the 
glomerulus is called the afferent arteriole. The branch that exits the 
glomerulus is called the efferent arteriole. Within the glomerulus, the 
network of capillaries is called the glomerular capillary bed. Once the 
efferent arteriole exits the glomerulus, it forms the peritubular capillary 
network, which surrounds and interacts with parts of the renal tubule. 


Kidney Function and Physiology 


Kidneys filter blood in a three-step process. First, the nephrons filter blood 
that runs through the capillary network in the glomerulus. Almost all 


solutes, except for proteins, are filtered out into the glomerulus by a process 
called glomerular filtration. The high arterial pressure and the permeable 
membranes of the glomerulus (see below) combine to accomplish this 
filtration. Second, the filtrate is collected in the renal tubules. Most of the 
solutes get reabsorbed in the PCT by a process called tubular 
reabsorption. In the loop of Henle, the filtrate continues to exchange 
solutes and water with the renal medulla and the peritubular capillary 
network. Water is also reabsorbed during this step. Then, additional solutes 
and wastes are secreted into the kidney tubules during tubular secretion, 
which is, in essence, the opposite process to tubular reabsorption. The 
collecting ducts collect filtrate coming from the nephrons and fuse in the 
medullary papillae. From here, the papillae deliver the filtrate, now called 
urine, into the minor calyces that eventually connect to the ureters through 
the renal pelvis. This entire process is illustrated in [link]. 


2. Proximal convoluted tubule: 
reabsorbs ions, water, and 
nutrients; removes toxins 
and adjusts filtrate pH 


5. Distal tubule: 
selectively secretes 
and absorbs different 
ions to maintain blood 
pH and electrolyte 
balance 


1. Glomerulus: 


filters small 

solutes from 

the blood 

6. Collecting 

duct: 
reabsorbs 
solutes and 
water from 


the filtrate 


4. Ascending loop 
of Henle: 
reabsorbs Na* and 
CF from the filtrate 
into the interstitial 
fluid 


3. Descending 
loop of Henle: 
aquaporins 
allow water 

to pass from 

) the filtrate 

into the 
interstitial fluid 


Each part of the nephron performs 
a different function in filtering 
waste and maintaining 


homeostatic balance. (1) The 
glomerulus forces small solutes 
out of the blood by pressure. (2) 
The proximal convoluted tubule 
reabsorbs ions, water, and 
nutrients from the filtrate into the 
interstitial fluid, and actively 
transports toxins and drugs from 
the interstitial fluid into the 
filtrate. The proximal convoluted 
tubule also adjusts blood pH by 
selectively secreting ammonia 
(NH3) into the filtrate, where it 
reacts with H* to form NH,". The 
more acidic the filtrate, the more 
ammonia is secreted. (3) The 
descending loop of Henle is lined 
with cells containing aquaporins 
that allow water to pass from the 
filtrate into the interstitial fluid. 
(4) In the thin part of the 
ascending loop of Henle, Na* and 
Cl ions diffuse into the interstitial 
fluid. In the thick part, these same 
ions are actively transported into 
the interstitial fluid. Because salt 
but not water is lost, the filtrate 
becomes more dilute as it travels 
up the limb. (5) In the distal 
convoluted tubule, K* and H™ ions 
are selectively secreted into the 
filtrate, while Na’, Cl’, and HCO3" 
ions are reabsorbed to maintain 
pH and electrolyte balance in the 
blood. (6) The collecting duct 
reabsorbs solutes and water from 
the filtrate, forming dilute urine. 


(credit: modification of work by 
NIDDK) 


Glomerular Filtration 


Glomerular filtration filters out most of the solutes due to high blood 
pressure and specialized membranes in the afferent arteriole. The blood 
pressure in the glomerulus is maintained independent of factors that affect 
systemic blood pressure. The “leaky” connections between the endothelial 
cells of the glomerular capillary network allow solutes to pass through 
easily. All solutes in the glomerular capillaries, except for macromolecules 
like proteins, pass through by passive diffusion. There is no energy 
requirement at this stage of the filtration process; high arterial blood 
pressure does the work at this stage. 


Tubular Reabsorption and Secretion 


Tubular reabsorption occurs in the PCT part of the renal tubule. Almost all 
nutrients (e.g. glucose, amino acids) are reabsorbed, and this occurs either 
by passive or active transport. Reabsorption of water and some key 
electrolytes are regulated and can be influenced by hormones. Sodium 
(Na‘) is the most abundant ion and most of it is reabsorbed by active 
transport and then transported to the peritubular capillaries. Because Na’ is 
actively transported out of the tubule, water follows it to even out the 
osmotic pressure. Water is also independently reabsorbed into the 
peritubular capillaries due to the presence of aquaporins, or water channels, 
in the PCT. This occurs due to the low blood pressure and high osmotic 
pressure in the peritubular capillaries. However, every solute has a transport 
maximum and the excess is not reabsorbed. 


In the loop of Henle, the permeability of the membrane changes. The 
descending limb is permeable to water, not solutes; the opposite is true for 
the ascending limb. Additionally, the loop of Henle invades the renal 


medulla, which is naturally high in salt concentration and tends to absorb 
water from the renal tubule and concentrate the filtrate. The osmotic 
gradient increases as it moves deeper into the medulla. Because two sides of 
the loop of Henle perform opposing functions, as illustrated in [link], it acts 
as a countercurrent multiplier. The vasa recta around it acts as the 
countercurrent exchanger. 


Filtrate enters the Filtrate exits the 
descending limb. ascending limb. 


Interstitial 


Loop of 
fluid 


Henle 


The loop of Henle acts as a 
countercurrent multiplier that 
uses energy to create 
concentration gradients. The 
descending limb is water 
permeable. Water flows from 
the filtrate to the interstitial 
fluid, so osmolality inside the 
limb increases as it descends 
into the renal medulla. At the 
bottom, the osmolality is 
higher inside the loop than in 
the interstitial fluid. Thus, as 
filtrate enters the ascending 
limb, Na* and CI ions exit 


through ion channels present 
in the plasma membrane. 
Further up, Na” is actively 

transported out of the filtrate 

and Cl follows. Osmolarity 

is given in units of 
milliosmoles per liter 
(mOsm/L). 


Hypertension (high blood pressure) is a common problem for humans, and 
is usually treated with a variety of drugs that act on various processes 
occurring in the kidney. One class of hypertension drugs is the so-called 
"loop diuretics", which inhibit the reabsorption of Na* and CI ions by the 
ascending limb of the loop of Henle. A side effect is that they increase 
urination. Why do you think this is the case? 


By the time the filtrate reaches the DCT, most of the urine and solutes have 
been reabsorbed. If the body requires additional water, all of it can be 
reabsorbed at this point. Further reabsorption is controlled by hormones, 
which will be discussed in a later section. Excretion of wastes occurs due to 
lack of reabsorption combined with tubular secretion. Undesirable products 
like metabolic wastes, urea, uric acid, and certain drugs, are excreted by 
tubular secretion. Most of the tubular secretion happens in the DCT, but 
some occurs in the early part of the collecting duct. Kidneys also maintain 
an acid-base balance by secreting excess H" ions. 


Nitrogenous Waste 


Of the four major macromolecules in biological systems, both proteins and 
nucleic acids contain nitrogen. During the catabolism, or breakdown, of 
nitrogen-containing macromolecules, carbon, hydrogen, and oxygen are 
extracted and stored in the form of carbohydrates and fats. Excess nitrogen 
is excreted from the body. Nitrogenous wastes tend to form toxic ammonia, 
which raises the pH of body fluids. The formation of ammonia itself 
requires energy in the form of ATP and large quantities of water to dilute it 


out of a biological system. It is quite toxic even at relatively low 
concentrations. Animals that live in aquatic environments tend to release 
ammonia directly into the water in the urine; they have access to sufficient 
water to dilute this waste product to non-toxic levels. Animals that excrete 
ammonia are said to be ammonotelic. Terrestrial organisms have evolved 
other mechanisms to process and excrete nitrogenous wastes. The animals 
first detoxify ammonia by converting it into a relatively nontoxic form such 
as urea or uric acid. Mammals, including humans, produce urea, whereas 
reptiles and many terrestrial invertebrates produce uric acid. Animals that 
secrete urea as the primary nitrogenous waste material are called ureotelic 
animals. 


Nitrogenous Waste in Terrestrial Animals: Urea 


Urea formation is the primary mechanism by which mammals convert 
ammonia to urea. Urea is made in the liver and excreted in urine. The 
overall chemical reaction by which ammonia is converted to urea is 2 NH3 
(ammonia) + CO, + 3 ATP + H»O —~ H»N-CO-NH)> (urea) + 2 ADP + 4 P; 
+ AMP. 


Note: 

Evolution Connection 

Excretion of Nitrogenous Waste 

The theory of evolution proposes that life started in an aquatic 
environment. It is not surprising to see that biochemical pathways like the 
urea cycle evolved to adapt to a changing environment when terrestrial life 
forms evolved. Arid conditions probably led to the evolution of the uric 
acid pathway as a means of conserving water. 


Nitrogenous Waste in Birds and Reptiles: Uric Acid 


Birds, reptiles, and most terrestrial arthropods convert toxic ammonia to 
uric acid or the closely related compound guanine (guano) instead of urea. 
Mammals also form some uric acid during breakdown of nucleic acids. Uric 
acid is a compound similar to purines found in nucleic acids. It is water 
insoluble and tends to form a white paste or powder; it is excreted by birds, 
insects, and reptiles. Conversion of ammonia to uric acid requires more 
energy and is much more complex than conversion of ammonia to urea 
[link], but the pay off is that uric acid requires much less water when 
excreted. 


a At NH, 
Zz Ammonia 
* a 5 


Uric acid 


LE. 
(a) Many invertebrates and (b) Mammals, many adult (c) Insects, land snails, birds, 
aquatic species excrete amphibians, and some marine and many reptiles excrete 
ammonia. species excrete urea. uric acid. 


Nitrogenous waste is excreted in different forms by different 
species. These include (a) ammonia, (b) urea, and (c) uric acid. 
(credit a: modification of work by Eric Engbretson, USFWS; 
credit b: modification of work by B. "Moose" Peterson, USFWS; 
credit c: David A. Rintoul) 


Gout 

In some animals, uric acid can build up under certain conditions, or as 
consequence of a diet high in nitrogenous compounds (e.g. nucleotides). In 
those situations, uric acid tends to crystallize and form kidney stones. Uric 
acid buildup may also cause a painful condition called gout, where uric acid 
crystals accumulate in the joints, as illustrated in [link]. Food choices that 
reduce the amount of nitrogenous compounds in the diet help reduce the 
risk of gout. For example, tea, coffee, and chocolate have purine-like 
compounds, called xanthines, and should be avoided by people with gout 
and kidney stones. 


Gout causes the inflammation visible 
in this person’s left big toe joint. 
(credit: "Gonzosft"/Wikimedia 
Commons) 


Musculoskeletal System 


Introduction 

"Of all the constituents of the human body, bone is the hardest, the driest, 
the earthiest and the coldest; and, excepting only the teeth, it is devoid of 
sensation. God, the great Creator of all things, formed its substance to this 
specification with good reason, intending it to be like a foundation for the 
whole body; for it the fabric of the human body bones perform the same 
function as do walls and beams in houses, poles in tents, and keels and ribs 
in boats." Andreas Vesalius, Flemish anatomist, in De Humanis Corporis 
Fabrica, 1543 


As Vesalius recognized long ago, the muscular and skeletal systems provide 
support to the body and allow for a wide range of movement. The bones of 
the skeletal system protect the body’s internal organs and support the 
weight of the body. The muscles of the muscular system contract and pull 
on the bones, allowing for movements as diverse as standing, walking, 
running, and grasping items. Injury or disease affecting the musculoskeletal 
system can be very debilitating. In humans, the most common 
musculoskeletal diseases worldwide are caused by malnutrition. Ailments 
that affect the joints are also widespread, such as arthritis, which can make 
movement difficult and—in advanced cases—completely impair mobility. 


Types of Skeletal Systems 


A skeletal system is necessary to support the body, protect internal organs, 
and allow for the movement of an organism. There are three different 
skeleton designs that fulfill these functions: hydrostatic skeleton, 
exoskeleton, and endoskeleton. 


Hydrostatic Skeleton 


A hydrostatic skeleton is a skeleton formed by a fluid-filled compartment 
within the body, called the coelom. The organs of the coelom are supported 
by the aqueous fluid, which also resists external compression. This 
compartment is under hydrostatic pressure because of the fluid and supports 


the other organs of the organism. This type of skeletal system is found in 
soft-bodied animals such as sea anemones, earthworms, Cnidaria, and other 
invertebrates ([link]). 


The skeleton of the red-knobbed 
sea star (Protoreaster linckii) is an 
example of a hydrostatic skeleton. 

(credit: “Amada44”/Wikimedia 

Commons) 


Movement in a hydrostatic skeleton is provided by muscles that surround 
the coelom. The muscles in a hydrostatic skeleton contract to change the 
shape of the coelom; the pressure of the fluid in the coelom produces 
movement. For example, earthworms move by waves of muscular 
contractions of the skeletal muscle of the body wall hydrostatic skeleton, 
called peristalsis, which alternately shorten and lengthen the body. 
Lengthening the body extends the anterior end of the organism. Most 
organisms have a mechanism to fix themselves in the substrate. Shortening 
the muscles then draws the posterior portion of the body forward. Although 
a hydrostatic skeleton is well-suited to invertebrate organisms such as 
earthworms and some aquatic organisms, it is not an efficient skeleton for 
terrestrial animals. 


Exoskeleton 


An exoskeleton is a chitinous external skeleton that consists of a hard 
encasement on the surface of an organism. For example, the shells of crabs 
and insects are exoskeletons ([link]). This skeleton type provides defense 
against predators, supports the body, and allows for movement through the 
contraction of attached muscles. As with endoskeletons (see below), 
muscles must cross a joint inside the exoskeleton. Shortening of the muscle 
thus changes the relationship of the two segments of the exoskeleton. 
Arthropods such as crabs and lobsters have exoskeletons that consist of 30— 
50 percent chitin, a polysaccharide derivative of glucose that is a strong but 
flexible material. Chitin is secreted by the epidermal cells. The exoskeleton 
is further strengthened by the addition of calcium carbonate in organisms 
such as the lobster. Because the exoskeleton is acellular, arthropods must 
periodically shed their exoskeletons as they grow, because the exoskeleton 
does not grow as the organism grows. 


Muscles attached to the 
exoskeleton of the Halloween crab 
(Gecarcinus quadratus) allow it to 

move. 


Endoskeleton 


An endoskeleton is a skeleton that consists of hard, mineralized structures 
located within the soft tissue of organisms. The bones of vertebrates are 
composed of tissues and mineralized tissues. Endoskeletons provide support 
for the body, protect internal organs, and allow for movement through 
contraction of muscles attached to the skeleton. 


The skeletons of humans and 
horses are examples of 
endoskeletons. (credit: Ross 
Murphy) 


As an example, the human skeleton is an endoskeleton that consists of 206 
bones in the adult. It has five main functions: providing support to the body, 
storing minerals and lipids, producing blood cells, protecting internal 


organs, and allowing for movement. The skeletal system in vertebrates is 
divided into the axial skeleton (which consists of the skull, vertebral 
column, and rib cage), and the appendicular skeleton (which consists of the 
shoulders, limb bones, the pectoral girdle, and the pelvic girdle). 


Main divisions of the vertebrate skeleton 


Ossicles 
(inner ear) 


Hyoid bone 


" 
u 


Ny 


Gi 
SS 
ane 


: 5 Na 
G NX iN 
(oo Lt 
A f i Wh >» 

QT sh 0 } ? 


Vertebral 
column 


C, 
77 A . 
CULE 


Ss, 
ul 


The axial skeleton of humans 
consists of the bones of the skull, 
ossicles of the middle ear, hyoid 

bone, vertebral column, and rib 
cage. (credit: modification of work 
by Mariana Ruiz Villareal) 


The human appendicular 
skeleton is composed of the 
bones of the pectoral limbs 

(arm, forearm, hand), the pelvic 
limbs (thigh, leg, foot), the 
pectoral girdle, and the pelvic 
girdle. (credit: modification of 
work by Mariana Ruiz 
Villareal) 


Evolution of Body Design for Locomotion on Land 


The transition of vertebrates from fish ancestors to land-dwelling animals 
required a number of changes in body design, since movement on land 
poses challenges that are different from those posed by movement in water. 
Water provides a certain amount of lift, which is missing on land, so 
muscles are needed to provide that lift on land. It also provides a medium to 
push against, and many fish use lateral undulations to push against the 
water and generate forward movement. Air does not provide the same 
resistance, and so lateral undulations on land would not produce much 
movement forward. 


As certain fish began to move onto land, they retained their lateral 
undulation form of locomotion. However, instead of pushing against water, 
their fins became points of contact with the ground, and the lateral 
undulations became rotations about those points of contact. The lack of 
bouyancy provided by water led to increased ossification of the bones and 
strengthening of the muscles, as well as providing selective pressure that 
resulted in changes in arrangement of the "wrist" bones of these early 
tetrapods. The effect of gravity also led to changes in the axial skeleton, 
since rotations around the contact points with the ground caused new 
torsional strains on the vertebral column. A firmer, more ossified vertebral 
column became common in land animals, because it reduces the strain and 
also provides strength to support the weight of the body. In later tetrapods 
the vertebrae began allowing for vertical rather than lateral flexing. The 
vertebrae of the neck also evolved to allow movement of the head 
independently of the body, a range of motion not found in fish. 


In early terrestrial tetrapods (({link]), the limbs were splayed out to the side, 
reflecting the position of the fins in their fishy ancestors. This resulted in a 
form of motion that was similar to performing push-ups while walking, 
which requires large muscles to move the limbs toward the midline. This is 
not an efficient form of locomotion, and selective pressures soon led to a 
configuration where the limbs were placed undermeath the body, so that 
each stride requires less energy to move the animal forward. The rotation 
around the point of contact became a motion that is more like a pendulum 
when the limbs are underneath the body, producing a stride that was much 


more efficient for movement over land. Additional changes were required 
in the appendicular skeleton to accommodate the new ranges of motion that 
were enabled by that limb placement. 


Muscles 


Muscle cells are specialized for contraction. Muscles allow for motions 
such as walking, and they also facilitate bodily processes such as respiration 
and digestion. The body contains three types of muscle tissue: skeletal 
muscle, cardiac muscle, and smooth muscle ((link]). 


Skeletal muscle Smooth muscle Cardiac muscle 


The body contains three types of muscle tissue: skeletal muscle, 
smooth muscle, and cardiac muscle, visualized here using light 
microscopy. Smooth muscle cells are short, tapered at each end, 
and have only one plump nucleus in each. Cardiac muscle cells 
are branched and striated, but short. The cytoplasm may branch, 
and they have one nucleus in the center of the cell. (credit: 
modification of work by NCI, NIH; scale-bar data from Matt 
Russell) 


Skeletal muscle tissue forms skeletal muscles, which attach to bones or 
skin and control locomotion and any movement that can be consciously 
controlled. Because it can be controlled by thought, skeletal muscle is also 
called voluntary muscle. Skeletal muscles are long and cylindrical in 
appearance; when viewed under a microscope, skeletal muscle tissue has a 
striped or striated appearance. The striations are caused by the regular 


arrangement of contractile proteins (actin and myosin). Actin is a globular 
contractile protein that interacts with myosin for muscle contraction. 
Skeletal muscle cells form by fusion of many muscle cells called myoblasts, 
and thus have multiple nuclei present in a single cell. 


Smooth muscle tissue occurs in the walls of hollow organs such as the 
intestines, stomach, and urinary bladder, and around passages such as the 
respiratory tract and blood vessels. Smooth muscle has no striations, is not 
under voluntary control, has only one nucleus per cell, is tapered at both 
ends, and is also called involuntary muscle. 


Cardiac muscle tissue is only found in the heart, and cardiac contractions 
pump blood throughout the body and maintain blood pressure. Like skeletal 
muscle, cardiac muscle is striated, but unlike skeletal muscle, cardiac 
muscle cannot be consciously controlled and is called involuntary muscle. It 
has one nucleus per cell, is branched, and is distinguished by the presence 
of intercalated disks. Intercalated disks are ion-permeable junctions 
between individual cardiac muscle cells which allow for synchronized 
contractions of the various regions of the heart. 


Skeletal Muscle Fiber Structure 


Each skeletal muscle fiber is a skeletal muscle cell. These cells are 
incredibly large, with diameters of up to 100 jm and lengths of up to 30 
cm. The plasma membrane of a skeletal muscle fiber is called the 
sarcolemma. The sarcolemma is the site of action potential conduction, 
which triggers muscle contraction. Within each muscle fiber are myofibrils 
—long cylindrical structures that lie parallel to the muscle fiber. Myofibrils 
run the entire length of the muscle fiber, and because they are only 
approximately 1.2 am in diameter, hundreds to thousands can be found 
inside one muscle fiber. They attach to the sarcolemma at their ends, so that 
as myofibrils shorten, the entire muscle cell contracts ([Link]). 


Sarcolemma 


Sarcoplasm 


Myofibrils 


Striations 


Muscle fiber 


A skeletal muscle cell is surrounded by a plasma membrane called 
the sarcolemma with a cytoplasm called the sarcoplasm. A muscle 
fiber is composed of many fibrils, packaged into orderly units. 


The striated appearance of skeletal muscle tissue is a result of repeating 
bands of the proteins actin and myosin that are present along the length of 
myofibrils. Dark A bands and light I bands repeat along myofibrils, and the 
alignment of myofibrils in the cell causes the entire cell to appear striated or 
banded. 


Each I band has a dense line running vertically through the middle called a 
Z disc or Z line. The Z discs mark the border of units called sarcomeres, 
which are the functional units of skeletal muscle. One sarcomere is the 
space between two consecutive Z discs and contains one entire A band and 
two halves of an I band, one on either side of the A band. A myofibril is 
composed of many sarcomeres running along its length, and as the 
sarcomeres individually contract, the myofibrils and muscle cells shorten 
({link]). 


Z line Sarcomere 


Thin filament Thick filament 


Myofibril 


A sarcomere is the region from 
one Z line to the next Z line. Many 
sarcomeres are present in a 
myofibril, resulting in the striation 
pattern characteristic of skeletal 
muscle. 


Myofibrils are composed of smaller structures called myofilaments. There 
are two main types of filaments: thick filaments and thin filaments; each 
has different compositions and locations. Thick filaments occur only in the 
A band of a myofibril. Thin filaments attach to a protein in the Z disc 
called alpha-actinin and occur across the entire length of the I band and 
partway into the A band. The region at which thick and thin filaments 
overlap has a dense appearance, as there is little space between the 
filaments. Thin filaments do not extend all the way into the A bands, 
leaving a central region of the A band that only contains thick filaments. 
This central region of the A band looks slightly lighter than the rest of the A 
band and is called the H zone. The middle of the H zone has a vertical line 
called the M line, at which accessory proteins hold together thick filaments. 
Both the Z disc and the M line hold myofilaments in place to maintain the 
structural arrangement and layering of the myofibril. Myofibrils are 
connected to each other by intermediate, or desmin, filaments that attach to 
the Z disc. 


Thick and thin filaments are themselves composed of proteins. Thick 
filaments are primarily composed of the protein myosin. The tail of a 
myosin molecule connects with other myosin molecules to form the central 
region of a thick filament near the M line, whereas the heads align on either 
side of the thick filament where the thin filaments overlap. The primary 
component of thin filaments is the actin protein. Two other components of 
the thin filament are tropomyosin and troponin. Actin has binding sites for 
myosin attachment. Strands of tropomyosin block the binding sites and 
prevent actin—myosin interactions when the muscles are at rest. Troponin 
consists of three globular subunits. One subunit binds to tropomyosin, one 
subunit binds to actin, and one subunit binds Ca2* ions. 


Sliding Filament Model of Contraction 


For a muscle cell to contract, the sarcomere must shorten. However, 
individual thick and thin filaments—the components of sarcomeres—do not 
shorten. Instead, they slide by one another, causing the sarcomere to shorten 
while the filaments remain the same length. The sliding filament theory of 
muscle contraction was developed to explain the differences observed in the 
lengths of the named bands on the sarcomere at different degrees of muscle 
contraction and relaxation. The mechanism of contraction is the binding of 
myosin to actin, forming cross-bridges that generate filament movement 
([link]). 


(a) Thin filament Thick filaments 


(actin) (myosin) 
Z line M line Z line 
Set bce e enema ceeeeeeceeeed 
eet: Se cae eee eeeeeeeeeeeee 
SH Saco e eee eeeeeeeee 
EEE ESEEEESEY TEES 
Settee >> 
See: > 
EERE TERS SESS 


(b) 


> —————— es | 


| band A band | band 


When (a) a sarcomere (b) contracts, the Z lines move closer 
together and the I band gets smaller. The A band stays the same 
width and, at full contraction, the thin filaments overlap. 


When a sarcomere shortens, some regions shorten whereas others stay the 
same length. A sarcomere is defined as the distance between two 
consecutive Z discs or Z lines; when a muscle contracts, the distance 
between the Z discs is reduced. The H zone—the central region of the A 
zone—contains only thick filaments and is shortened during contraction. 
The I band contains only thin filaments and also shortens. The A band does 
not shorten—it remains the same length—but A bands of different 
sarcomeres move closer together during contraction, eventually 


disappearing. Thin filaments are pulled by the thick filaments toward the 
center of the sarcomere until the Z discs approach the thick filaments. The 
zone of overlap, in which thin filaments and thick filaments occupy the 
same area, increases as the thin filaments move inward. 


ATP and Muscle Contraction 


The motion of muscle shortening occurs as myosin heads bind to actin and 
pull the actin inwards. This action requires energy, which is provided by 
ATP. Myosin binds to actin at a binding site on the globular actin protein. 
Myosin has another binding site for ATP, and acts as an enzyme to convert 
ATP to ADP, releasing an inorganic phosphate molecule and energy. The 
energy can be harnessed to promote contraction via the sliding filament 
mechanism described above. 


ATP binding causes myosin to release actin, allowing actin and myosin to 
detach from each other. After this happens, the newly bound ATP is 
converted to ADP and inorganic phosphate, P;. The enzyme at the binding 
site on myosin is called ATPase. The energy released during ATP hydrolysis 
changes the angle of the myosin head into a “cocked” position. The myosin 
head is then in a position for further movement, possessing potential energy, 
but ADP and P; are still attached. If actin binding sites are covered and 
unavailable, the myosin will remain in the high energy configuration with 
ATP hydrolyzed, but still attached. 


If the actin binding sites are uncovered, a cross-bridge will form; that is, the 
myosin head spans the distance between the actin and myosin molecules. P; 
is then released, allowing myosin to expend the stored energy as a 
conformational change. The myosin head moves toward the M line, pulling 
the actin along with it. As the actin is pulled, the filaments move 
approximately 10 nm toward the M line. This movement is called the power 
stroke, as it is the step at which force is produced. As the actin is pulled 
toward the M line, the sarcomere shortens and the muscle contracts. 


When the myosin head is “cocked,” it contains energy and is in a high- 
energy configuration. This energy is expended as the myosin head moves 


through the power stroke; at the end of the power stroke, the myosin head is 
in a low-energy position. After the power stroke, ADP is released; however, 
the cross-bridge formed is still in place, and actin and myosin are bound 
together. ATP can then attach to myosin, which allows the cross-bridge 
cycle to start again and further muscle contraction can occur ([link]). 


Tropomyosin 


Ca2+ 


The active site on actin is 
exposed as Ca?* binds or 
troponin. Active site 


Myosin head A Actin 


@ The myosin head forms 
a cross-bridge with actin. 


During the power stroke, 

® the myosin head bends, 
and ADP and phosphate 
are released. 


Anew molecule of ATP 
0) attaches to the myosin 

head, causing the 

cross-bridge to detach. 


ATP hydrolyzes to ADP 
6) and phosphate, which 

returns the myosin to the 

“cocked” position. 


The cross-bridge muscle 
contraction cycle, which is 
triggered by Ca** binding to the 
actin active site, is shown. With 
each contraction cycle, actin 
moves relative to myosin, and the 
thick and thin filaments slide past 
each other. 


Regulatory Proteins 


When a muscle is in a resting state, actin and myosin are separated. To keep 
actin from binding to the active site on myosin, regulatory proteins block 
the molecular binding sites. Tropomyosin blocks myosin binding sites on 
actin molecules, preventing cross-bridge formation and preventing 
contraction in a muscle without nervous input. Troponin binds to 
tropomyosin and helps to position it on the actin molecule; it also binds 
calcium ions. 


To enable a muscle contraction, tropomyosin must change conformation, 
uncovering the myosin-binding site on an actin molecule and allowing 
cross-bridge formation. This can only happen in the presence of calcium, 
which is kept at extremely low concentrations in the sarcoplasm. If present, 
calcium ions bind to troponin, causing conformational changes in troponin 
that allow tropomyosin to move away from the myosin binding sites on 
actin. Once the tropomyosin is removed, a cross-bridge can form between 
actin and myosin, triggering contraction. Cross-bridge cycling continues 
until Ca** ions and ATP are no longer available and tropomyosin again 
covers the binding sites on actin. 


Excitation—Contraction Coupling 


Excitation—contraction coupling is the link (transduction) between the 
action potential generated in the sarcolemma and the start of a muscle 
contraction. The trigger for calcium release from the sarcoplasmic 
reticulum into the sarcoplasm is a neural signal. Each skeletal muscle fiber 
is controlled by a motor neuron, which conducts signals from the brain or 
spinal cord to the muscle. The area of the sarcolemma on the muscle fiber 
that interacts with the neuron is called the motor end plate. The end of the 
neuron’s axon is called the synaptic terminal, and it does not actually 


contact the motor end plate. A small space called the synaptic cleft 
separates the synaptic terminal from the motor end plate. Electrical signals 
travel along the neuron’s axon, which branches through the muscle and 
connects to individual muscle fibers at a neuromuscular junction. This 
junction is functionally similar to a synapse between two nerve cells, 
allowing a signal from the nerve cell to initiate an action potential in the 
muscle plasma membrane. The action potential in the muscle cell causes 
Ca** to be released from intracellular stores; this elevated calcium 
concentration triggers the binding of actin and myosin, ATP hyrolysis, and 
all of the other steps in contraction that are outlined above. 


The neurotransmitter released at the neuromuscular junction in most 
animals is acetylcholine. It is released from the nerve call ending and binds 
to receptors on the muscle cell plasma membrane ((link]); these receptors 
act as sodium channels when acetylcholine is bound to them. The influx of 
sodium depolarizes the muscle cell, triggering an action potential in a 
similar fashion to the action potential found in nerve cells. The 
acetylcholine is rapidly degraded in the neuromuscular junction by an 
enzyme called acetylcholinesterase. Various natural toxins (such as the 
curare used on poison arrows by South American indigenous tribes) and 
synthetic toxins (including nerve gases and insecticides) target the 
components of the neuromuscular junction, including both the receptor and 
the acetylcholinesterase. The deadly nerve gas known as Sarin irreversibly 
inhibits acetylcholinesterase. What effect would Sarin have on muscle 
contraction, and how does that effect lead to death? 


(a) 


Axon terminal 


Synaptic vesicles 


; Sarcolemma 
Acetylcholine (muscle cell 
receptor plasma 


Synaptic cleft membrane) 


Acetylcholine Acetylcholine 


Acetylcholinesterase 


Sarcoplasmic 
reticulum 
(muscle cell 
endoplasmic 
reticulum) 
1. Acetylcholine released from the axon 5. Acetylcholinesterase removes acetylcholine 
terminal binds to receptors on the from the synaptic cleft. 
sarcolemma. 6. Ca?* is transported back into the 
2. An action potential is generated and travels sarcoplasmic reticulum. 
down the T tubule. 7. Tropomyosin binds active sites on actin 
3. Ca?* is released from the sarcoplasmic causing the cross-bridge to detach. 
reticulum in response to the change in 
voltage. 


4. Ca?* binds troponin; Cross-bridges form 
between actin and myosin. 


Acetylcholine effects at the neuromuscular 
junction. The depolarization of the muscle plasma 
membrane releases calcium from the sarcoplasmic 

reticulum and initiates contraction of the muscle.